add collection-species to data import and tests

ccdb/species/factories.py

@@ -1,7 +1,8 @@
-from factory import DjangoModelFactory, Sequence
+from factory import DjangoModelFactory, Sequence, SubFactory
-from factory.fuzzy import FuzzyText, FuzzyChoice
+from factory.fuzzy import FuzzyText, FuzzyChoice, FuzzyInteger
 
-from .models import Species
+from .models import Species, CollectionSpecies
+from ..collections_ccdb.factories import CollectionFactory
 
 
 class SpeciesFactory(DjangoModelFactory):
@@ -13,3 +14,14 @@ class SpeciesFactory(DjangoModelFactory):
     species = FuzzyText(length=50)
     parasite = FuzzyChoice(choices=[True, False])
     sort_order = Sequence(lambda n: n)
+
+
+class CollectionSpeciesFactory(DjangoModelFactory):
+    class Meta:
+        model = CollectionSpecies
+
+    collection = SubFactory(CollectionFactory)
+    species = SubFactory(SpeciesFactory)
+    sex = FuzzyText(length=25)
+    count = FuzzyInteger(0)
+    count_estimated = FuzzyChoice(choices=[True, False])

ccdb/species/migrations/0005_DATA_species_collection.py

@@ -0,0 +1,41 @@
+from django.db import migrations
+from django.forms import modelform_factory
+
+from ccdb.utils.data import get_data_sources
+
+
+class Migration(migrations.Migration):
+    def migrate(apps, schema_editor):
+        sources = get_data_sources()
+        if not sources:
+            return
+
+        c = sources['db0']
+
+        CollectionSpecies = apps.get_model('species', 'CollectionSpecies')
+
+        CollectionSpecies.objects.all().delete()
+
+        CollectionSpeciesForm = modelform_factory(CollectionSpecies, fields='__all__')
+
+        for r in c.execute('SELECT * FROM tbl_hash_collection_species;'):
+            form = CollectionSpeciesForm(dict(collection=r[0], species=r[1], sex=r[2],
+                                    count=r[3], count_estimated=r[4]))
+            if form.is_valid():
+                # No PK in Andre's file
+                form.save()
+            else:
+                print('collection species', r[0:], form.errors.as_data())
+
+    def rollback(apps, schema_editor):
+        CollectionSpecies = apps.get_model('species', 'CollectionSpecies')
+        CollectionSpecies.objects.all().delete()
+
+    dependencies = [
+        ('species', '0004_DATA_initial'),
+        ('collections_ccdb', '0005_DATA_initial'),
+    ]
+
+    operations = [
+        migrations.RunPython(migrate, rollback),
+    ]

ccdb/species/tests/test_models.py

@@ -1,8 +1,8 @@
 from django.test import TestCase
 from django.db import IntegrityError, transaction
 
-from ..models import Species
+from ..models import Species, CollectionSpecies
-from ..factories import SpeciesFactory
+from ..factories import SpeciesFactory, CollectionSpeciesFactory
 
 
 class SpeciesTestCase(TestCase):
@@ -17,3 +17,18 @@ class SpeciesTestCase(TestCase):
             SpeciesFactory(common_name=s1.common_name, species=s1.species)
         s3 = SpeciesFactory()
         self.assertTrue(isinstance(s3, Species))
+
+
+class CollectionSpeciesTestCase(TestCase):
+    def test_creation(self):
+        c = CollectionSpeciesFactory()
+        self.assertTrue(isinstance(c, CollectionSpecies))
+        label = "{} {}".format(c.collection, c.species)
+        self.assertEqual(c.__str__(), label)
+
+    def test_uniqueness(self):
+        c1 = CollectionSpeciesFactory()
+        with transaction.atomic(), self.assertRaises(IntegrityError):
+            CollectionSpeciesFactory(collection=c1.collection, species=c1.species)
+        c3 = CollectionSpeciesFactory()
+        self.assertTrue(isinstance(c3, CollectionSpecies))