Merge pull request #10 from CIAT-DAPA/develop

Develop

Author: jchemutt

src/__init__.py

@@ -1,4 +1,5 @@
 from .ormgap.models.accession import Accession
 from .ormgap.models.crop import Crop
 from .ormgap.models.country import Country
-from .ormgap.models.group import Group
+from .ormgap.models.group import Group
+from .ormgap.models.project import Project

src/ormgap/__init__.py

@@ -2,4 +2,5 @@
 from .models.accession import Accession
 from .models.country import Country
 from .models.crop import Crop
-from .models.group import Group
+from .models.group import Group
+from .models.project import Project

src/ormgap/models/__init__.py

@@ -1,4 +1,5 @@
 from .accession import Accession
 from .country import Country
 from .crop import Crop
-from .group import Group
+from .group import Group
+from .project import Project

src/ormgap/models/accession.py

@@ -2,6 +2,7 @@
 from .crop import Crop
 from .group import Group
 from .country import Country
+from .project import Project
 
 class Accession(Document):
 
@@ -32,6 +33,8 @@ class Accession(Document):
         External identifier for the accession. Mandatory and unique.
     other_attributes: dict
         Additional attributes of the accession. Optional.
+    project: Project
+        Project object, project to which the accession is linked. Optional.    
     
     Methods:
     -------
@@ -46,12 +49,13 @@ class Accession(Document):
     }
     species_name = StringField(max_length=150)
     crop = ReferenceField(Crop, required=True)
-    landrace_group = ReferenceField(Group, required=True)
+    landrace_group = ReferenceField(Group, required=False)
     institution_name = StringField(max_length=255)
     source_database = StringField(max_length=255)
     country = ReferenceField(Country, required=True)
     latitude = FloatField(required=True)
     longitude = FloatField(required=True)
     accession_id = StringField(max_length=255)
     ext_id = StringField(max_length=255, required=True, unique=True)
+    project = ReferenceField(Project, required=False)
     other_attributes = DictField()

src/ormgap/models/project.py

@@ -0,0 +1,26 @@
+from mongoengine import Document, StringField
+
+class Project(Document):
+    """
+    Represents a project in the database.
+
+    Attributes:
+    ----------
+    ext_id: str
+        External identifier for the project. Mandatory and unique.
+    name: str
+        Name of the project. Mandatory.
+
+    Methods:
+    -------
+    save()
+        Saves the Project object to the database.
+    delete()
+        Deletes the Project object from the database.
+    """
+
+    meta = {
+        'collection': 'project'
+    }
+    ext_id = StringField(max_length=100, unique=True, required=True)
+    name = StringField(max_length=150, required=True)

src/tests/test_accession.py

@@ -11,6 +11,7 @@
 from ormgap.models.crop import Crop
 from ormgap.models.group import Group
 from ormgap.models.country import Country
+from ormgap.models.project import Project
 
 class AccessionTestCase(unittest.TestCase):
     @classmethod
@@ -24,6 +25,8 @@ def setUp(self):
         self.assertIsNotNone(self.group.id)
         self.country = Country(iso_2='AR',  name='Argentina').save()
         self.assertIsNotNone(self.country.id)
+        self.project = Project(name='Test Project', ext_id='P001').save()
+        self.assertIsNotNone(self.project.id)
         self.accession = Accession(
             species_name='Test Species', 
             crop=self.crop, 
@@ -34,7 +37,8 @@ def setUp(self):
             latitude=40.7128,
             longitude=-74.0060,
             accession_id='12345',
-            ext_id='123'
+            ext_id='123',
+            project=self.project
         )
 
     def test_create_accession(self):
@@ -47,6 +51,7 @@ def test_create_accession(self):
         self.assertEqual(accession.landrace_group.id, self.group.id)
         self.assertEqual(accession.latitude, 40.7128)
         self.assertEqual(accession.longitude, -74.0060)
+        self.assertEqual(accession.project.id, self.project.id)
 
 
     def test_get_accession_by_crop(self):
@@ -114,6 +119,7 @@ def tearDown(self):
         self.crop.delete()
         self.group.delete()
         self.country.delete()
+        self.project.delete()
         Accession.objects.delete()
 
 if __name__ == '__main__':

src/tests/test_project.py

@@ -0,0 +1,66 @@
+import unittest
+import sys
+import os
+
+dir_path = os.path.dirname(os.path.realpath(__file__))
+orm_dir_path = os.path.abspath(os.path.join(dir_path, '..'))
+sys.path.append(orm_dir_path)
+
+from mongoengine import connect, disconnect
+from ormgap.models.project import Project
+
+class ProjectTestCase(unittest.TestCase):
+    @classmethod
+    def setUpClass(cls):
+        """ Connect to a mock MongoDB instance. """
+        connect('test_gap_analysis', host='mongomock://localhost')
+
+    def setUp(self):
+        """ Clean up the database before each test. """
+        Project.objects.delete()
+        self.project = Project(ext_id='P001', name='Test Project')
+    
+    def test_create_project(self):
+        """ Test if a project is created successfully. """
+        self.project.save()
+        self.assertIsNotNone(self.project.id)
+    
+    def test_duplicate_ext_id(self):
+        """ Test that a project with duplicate ext_id is not allowed. """
+        self.project.save()
+        duplicate_project = Project(ext_id='P001', name='Duplicate Project')
+        with self.assertRaises(Exception) as context:
+            duplicate_project.save()
+        self.assertTrue('E11000 Duplicate Key Error' in str(context.exception))
+
+    def test_get_project_by_ext_id(self):
+        """ Test retrieving a project by ext_id. """
+        self.project.save()
+        project = Project.objects(ext_id='P001').first()
+        self.assertIsNotNone(project)
+        self.assertEqual(project.name, 'Test Project')
+
+    def test_update_project_name(self):
+        """ Test updating the project's name. """
+        self.project.save()
+        self.project.name = 'Updated Project'
+        self.project.save()
+
+        updated_project = Project.objects(ext_id='P001').first()
+        self.assertEqual(updated_project.name, 'Updated Project')
+
+    def test_delete_project(self):
+        """ Test deleting a project. """
+        self.project.save()
+        self.project.delete()
+
+        project = Project.objects(ext_id='P001').first()
+        self.assertIsNone(project)
+
+    @classmethod
+    def tearDownClass(cls):
+        """ Disconnect the mock database after all tests. """
+        disconnect()
+
+if __name__ == '__main__':
+    unittest.main()