experiments: data import and tests
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4 changed files with 203 additions and 3 deletions
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@ -77,7 +77,7 @@ class TreatmentReplicateFactory(DjangoModelFactory):
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class Meta:
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model = TreatmentReplicate
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treatment_replicate = SubFactory(TreatmentFactory)
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treatment = SubFactory(TreatmentFactory)
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name = Sequence(lambda n: 'treatment_replicate{}'.format(n))
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setup_date = FuzzyDate(date(2012, 1, 1))
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setup_time = LazyFunction(time)
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@ -90,7 +90,7 @@ class AliveDeadCountFactory(DjangoModelFactory):
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class Meta:
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model = AliveDeadCount
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treatment_replicate = SubFactory(TreatmentFactory)
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treatment_replicate = SubFactory(TreatmentReplicateFactory)
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status_date = FuzzyDate(date(2012, 1, 1))
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status_time = LazyFunction(time)
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count_alive = FuzzyInteger(0)
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113
ccdb/experiments/migrations/0009_DATA_initial.py
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113
ccdb/experiments/migrations/0009_DATA_initial.py
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@ -0,0 +1,113 @@
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from django.db import migrations
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from django.forms import modelform_factory
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from ccdb.utils.data import get_data_sources
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class Migration(migrations.Migration):
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def migrate(apps, schema_editor):
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sources = get_data_sources()
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if not sources:
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return
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c = sources['db0']
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Flaw = apps.get_model('experiments', 'Flaw')
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Experiment = apps.get_model('experiments', 'Experiment')
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TreatmentType = apps.get_model('experiments', 'TreatmentType')
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Treatment = apps.get_model('experiments', 'Treatment')
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TreatmentReplicate = apps.get_model('experiments', 'TreatmentReplicate')
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AliveDeadCount = apps.get_model('experiments', 'AliveDeadCount')
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for model in [AliveDeadCount, TreatmentReplicate, Treatment, TreatmentType,
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Experiment, Flaw]:
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model.objects.all().delete()
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ExperimentForm = modelform_factory(Experiment, exclude=('collections',))
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TreatmentTypeForm = modelform_factory(TreatmentType, fields='__all__')
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TreatmentForm = modelform_factory(Treatment, fields='__all__')
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TreatmentReplicateForm = modelform_factory(TreatmentReplicate, fields='__all__')
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AliveDeadCountForm = modelform_factory(AliveDeadCount, fields='__all__')
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for r in c.execute('SELECT * FROM tbl_lu_experiments;'):
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form = ExperimentForm(dict(name=r[1], code=r[2], description=r[3],
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sort_order=int(r[4]) if r[4] else None))
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if form.is_valid():
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Experiment.objects.create(id=r[0], **form.cleaned_data)
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else:
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print('experiment', r[0:], form.errors.as_data())
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for r in c.execute('SELECT * FROM tbl_lu_treatment_types;'):
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form = TreatmentTypeForm(dict(experiment=r[0], name=r[2], code=r[3],
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treatment_type=r[4], placement=r[5],
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description=r[6]))
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if form.is_valid():
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TreatmentType.objects.create(id=r[1], **form.cleaned_data)
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else:
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print('treatment type', r[0:], form.errors.as_data())
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for r in c.execute('SELECT * FROM tbl_treatments;'):
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form = TreatmentForm(dict(treatment_type=r[1], container=r[2],
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study_location=r[3], species=r[4], sex=r[5]))
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if form.is_valid():
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Treatment.objects.create(id=r[0], **form.cleaned_data)
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else:
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print('treatment', r[0:], form.errors.as_data())
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for r in c.execute('''
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SELECT *, setup_date AS "setup_date [dtdt]"
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FROM tbl_treatment_replicates tr
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LEFT OUTER JOIN tbl_lu_record_flaws f ON f.flawid=tr.flawid;
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'''):
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flaw = None
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if r[7]:
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flaw = Flaw.objects.create(name=r[10]).pk
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form = TreatmentReplicateForm(dict(treatment=r[0], name=r[2],
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setup_date=r[13],
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setup_sample_size=r[5], mass_g=r[6],
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flaw=flaw))
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if form.is_valid():
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TreatmentReplicate.objects.create(id=r[1], **form.cleaned_data)
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else:
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print('treatment replicate', r[0:], form.errors.as_data())
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for r in c.execute('''
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SELECT *,
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status_date AS "status_date [dtdt]",
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status_time AS "status_time [dtdt]"
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FROM tbl_alive_dead_counts adc
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LEFT OUTER JOIN tbl_lu_record_flaws f ON f.flawid=adc.flawid;
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'''):
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flaw = None
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if r[6]:
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flaw = Flaw.objects.create(name=r[9]).pk
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form = AliveDeadCountForm(dict(treatment_replicate=r[0],
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status_date=r[12],
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status_time=r[13].time() if r[13] else None,
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count_alive=r[4], count_dead=r[5],
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flaw=flaw))
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if form.is_valid():
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AliveDeadCount.objects.create(id=r[1], **form.cleaned_data)
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else:
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print('alive-dead count', r[0:], form.errors.as_data())
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def rollback(apps, schema_editor):
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Flaw = apps.get_model('experiments', 'Flaw')
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Experiment = apps.get_model('experiments', 'Experiment')
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TreatmentType = apps.get_model('experiments', 'TreatmentType')
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Treatment = apps.get_model('experiments', 'Treatment')
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TreatmentReplicate = apps.get_model('experiments', 'TreatmentReplicate')
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AliveDeadCount = apps.get_model('experiments', 'AliveDeadCount')
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for model in [AliveDeadCount, TreatmentReplicate, Treatment, TreatmentType,
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Experiment, Flaw]:
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model.objects.all().delete()
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dependencies = [
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('experiments', '0008_treatment_display_name'),
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('collections_ccdb', '0005_DATA_initial'),
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]
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operations = [
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migrations.RunPython(migrate, rollback),
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]
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@ -91,7 +91,7 @@ class TreatmentReplicate(models.Model):
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def save(self, *args, **kwargs):
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self.display_name = "{}_{}_{}_{}".format(self.treatment,
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self.setup_date.date(), self.name,
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self.setup_date, self.name,
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self.setup_sample_size)
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super(TreatmentReplicate, self).save(*args, **kwargs)
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@ -0,0 +1,87 @@
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from django.test import TestCase
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from django.db import IntegrityError, transaction
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from ..models import Flaw, Experiment, ProtocolAttachment, TreatmentType, \
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Treatment, TreatmentReplicate, AliveDeadCount
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from ..factories import FlawFactory, ExperimentFactory, ProtocolAttachmentFactory, \
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TreatmentTypeFactory, TreatmentFactory, TreatmentReplicateFactory, \
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AliveDeadCountFactory
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class FlawTestCase(TestCase):
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def test_creation(self):
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f = FlawFactory()
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self.assertTrue(isinstance(f, Flaw))
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self.assertEqual(f.__str__(), f.name)
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class ExperimentTestCase(TestCase):
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def test_creation(self):
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e = ExperimentFactory()
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self.assertTrue(isinstance(e, Experiment))
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self.assertEqual(e.__str__(), e.name)
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def test_uniqueness(self):
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e1 = ExperimentFactory()
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with transaction.atomic(), self.assertRaises(IntegrityError):
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ExperimentFactory(name=e1.name, code=e1.code)
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e3 = ExperimentFactory()
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self.assertTrue(isinstance(e3, Experiment))
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class ProtocolAttachmentTestCase(TestCase):
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def test_creation(self):
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p = ProtocolAttachmentFactory()
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self.assertTrue(isinstance(p, ProtocolAttachment))
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self.assertEqual(p.__str__(), p.protocol)
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class TreatmentTypeTestCase(TestCase):
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def test_creation(self):
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t = TreatmentTypeFactory()
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self.assertTrue(isinstance(t, TreatmentType))
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label = "{} {} {} {}".format(t.experiment, t.name, t.treatment_type,
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t.placement)
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self.assertEqual(t.__str__(), label)
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def test_uniqueness(self):
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t1 = TreatmentTypeFactory()
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with transaction.atomic(), self.assertRaises(IntegrityError):
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TreatmentTypeFactory(name=t1.name, experiment=t1.experiment)
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t3 = TreatmentTypeFactory()
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self.assertTrue(isinstance(t3, TreatmentType))
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class TreatmentTestCase(TestCase):
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def test_creation(self):
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t = TreatmentFactory()
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self.assertTrue(isinstance(t, Treatment))
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label = "{}_{}_{}_{}".format(t.treatment_type, t.study_location,
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t.species, t.sex)
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self.assertEqual(t.__str__(), label)
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class TreatmentReplicateTestCase(TestCase):
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def test_creation(self):
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t = TreatmentReplicateFactory()
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self.assertTrue(isinstance(t, TreatmentReplicate))
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label = "{}_{}_{}_{}".format(t.treatment, t.setup_date,
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t.name, t.setup_sample_size)
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self.assertEqual(t.__str__(), label)
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def test_uniqueness(self):
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t1 = TreatmentReplicateFactory()
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with transaction.atomic(), self.assertRaises(IntegrityError):
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TreatmentReplicateFactory(treatment=t1.treatment, name=t1.name,
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setup_date=t1.setup_date,
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setup_time=t1.setup_time)
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t3 = TreatmentReplicateFactory()
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self.assertTrue(isinstance(t3, TreatmentReplicate))
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class AliveDeadCountTestCase(TestCase):
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def test_creation(self):
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a = AliveDeadCountFactory()
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self.assertTrue(isinstance(a, AliveDeadCount))
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label = "{}".format(a.status_date)
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self.assertEqual(a.__str__(), label)
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