collections: tests and data migration
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5 changed files with 290 additions and 2 deletions
88
ccdb/collections_ccdb/factories.py
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88
ccdb/collections_ccdb/factories.py
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from datetime import date, time
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from factory import DjangoModelFactory, Sequence, SubFactory, LazyFunction
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from factory.fuzzy import FuzzyText, FuzzyDate, FuzzyInteger
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from factory.django import FileField
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from .models import CollectionType, CollectionMethod, Flaw, ADFGPermit, Collection, \
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DatasheetAttachment, CollectionTrap
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from ..projects.factories import ProjectFactory
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from ..locations.factories import StudyLocationFactory, StorageLocationFactory
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from ..processing.factories import ProcessTypeFactory, ReagentFactory
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class CollectionTypeFactory(DjangoModelFactory):
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class Meta:
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model = CollectionType
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name = Sequence(lambda n: 'collection_type{}'.format(n))
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code = Sequence(lambda n: 'ct{}'.format(n))
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sort_order = Sequence(lambda n: n)
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class CollectionMethodFactory(DjangoModelFactory):
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class Meta:
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model = CollectionMethod
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name = Sequence(lambda n: 'collection_method{}'.format(n))
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code = Sequence(lambda n: 'cm{}'.format(n))
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collection_method_class = FuzzyText(length=50)
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sort_order = Sequence(lambda n: n)
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class FlawFactory(DjangoModelFactory):
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class Meta:
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model = Flaw
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name = Sequence(lambda n: 'flaw{}'.format(n))
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description = FuzzyText(length=255)
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sort_order = Sequence(lambda n: n)
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class ADFGPermitFactory(DjangoModelFactory):
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class Meta:
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model = ADFGPermit
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name = Sequence(lambda n: 'adfg_permit{}'.format(n))
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sort_order = Sequence(lambda n: n)
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class CollectionFactory(DjangoModelFactory):
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class Meta:
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model = Collection
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project = SubFactory(ProjectFactory)
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study_location = SubFactory(StudyLocationFactory)
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collection_type = SubFactory(CollectionTypeFactory)
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collection_method = SubFactory(CollectionMethodFactory)
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number_of_traps = FuzzyInteger(0)
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collection_start_date = FuzzyDate(date(2012, 1, 1))
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collection_start_time = None
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collection_end_date = FuzzyDate(date(2015, 1, 1))
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collection_end_time = None
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storage_location = SubFactory(StorageLocationFactory)
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specimen_state = FuzzyText(length=50)
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process_type = SubFactory(ProcessTypeFactory)
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reagent = SubFactory(ReagentFactory)
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adfg_permit = SubFactory(ADFGPermitFactory)
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flaw = SubFactory(FlawFactory)
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class DatasheetAttachmentFactory(DjangoModelFactory):
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class Meta:
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model = DatasheetAttachment
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collection = SubFactory(CollectionFactory)
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datasheet = FileField()
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class CollectionTrapFactory(DjangoModelFactory):
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class Meta:
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model = CollectionTrap
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collection = SubFactory(CollectionFactory)
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number_of_traps = FuzzyInteger(0)
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date_opened = FuzzyDate(date(2012, 1, 1))
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time_opened = LazyFunction(time)
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date_closed = FuzzyDate(date(2015, 1, 1))
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time_closed = LazyFunction(time)
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107
ccdb/collections_ccdb/migrations/0005_DATA_initial.py
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107
ccdb/collections_ccdb/migrations/0005_DATA_initial.py
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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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CollectionType = apps.get_model('collections_ccdb', 'CollectionType')
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CollectionMethod = apps.get_model('collections_ccdb', 'CollectionMethod')
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Flaw = apps.get_model('collections_ccdb', 'Flaw')
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ADFGPermit = apps.get_model('collections_ccdb', 'ADFGPermit')
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Collection = apps.get_model('collections_ccdb', 'Collection')
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DatasheetAttachment = apps.get_model('collections_ccdb', 'DatasheetAttachment')
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CollectionTrap = apps.get_model('collections_ccdb', 'CollectionTrap')
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for model in [CollectionTrap, Collection, Flaw, DatasheetAttachment,
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CollectionMethod, CollectionType, ADFGPermit]:
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model.objects.all().delete()
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Project = apps.get_model('projects', 'Project')
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CollectionTypeForm = modelform_factory(CollectionType, fields='__all__')
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CollectionMethodForm = modelform_factory(CollectionMethod, fields='__all__')
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ADFGPermitForm = modelform_factory(ADFGPermit, fields='__all__')
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CollectionForm = modelform_factory(Collection, fields='__all__')
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for r in c.execute('SELECT * FROM tbl_lu_collection_types;'):
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form = CollectionTypeForm(dict(name=r[1], code=r[2],
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sort_order=int(r[3]) if r[3] else None))
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if form.is_valid():
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CollectionType.objects.create(id=r[0], **form.cleaned_data)
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else:
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print('collection type', r[0:], form.errors.as_data())
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for r in c.execute('SELECT * FROM tbl_lu_collection_methods;'):
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form = CollectionMethodForm(dict(name=r[1], code=r[2],
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collection_method_class=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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CollectionMethod.objects.create(id=r[0], **form.cleaned_data)
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else:
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print('collection method', r[0:], form.errors.as_data())
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for i, r in enumerate(c.execute('SELECT DISTINCT ADFG_Permit FROM tbl_collections;')):
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form = ADFGPermitForm(dict(name=r[0], sort_order=i))
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if form.is_valid():
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form.save()
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else:
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print('adfg permit', r[0:], form.errors.as_data())
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for r in c.execute('''
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SELECT *,
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collection_start_date AS "collection_start_date [dtdt]",
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collection_start_time AS "collection_start_time [dtdt]",
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collection_end_date AS "collection_end_date [dtdt]",
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collection_end_time AS "collection_end_time [dtdt]"
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FROM tbl_collections;
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'''):
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permit = None
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if r[14] is not '':
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permit = ADFGPermit.objects.get(name=r[14]).pk
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form = CollectionForm(dict(project=r[0], study_location=r[2],
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collection_type=r[3], collection_method=r[4],
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number_of_traps=r[5],
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collection_start_date=r[17],
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collection_start_time=r[18].time() if r[18] else None,
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collection_end_date=r[19],
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collection_end_time=r[20].time() if r[20] else None,
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storage_location=r[10], specimen_state=r[11],
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process_type=r[12], reagent=r[13],
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adfg_permit=permit))
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if form.is_valid():
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project = Project.objects.get(id=r[0])
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d = "{}_{}_{}_{}".format(project, form.cleaned_data['collection_end_date'],
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form.cleaned_data['study_location'],
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form.cleaned_data['collection_type'])
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Collection.objects.create(id=r[1], display_name=d, **form.cleaned_data)
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else:
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print('collection', r[0:], form.errors.as_data())
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def rollback(apps, schema_editor):
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CollectionType = apps.get_model('collections_ccdb', 'CollectionType')
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CollectionMethod = apps.get_model('collections_ccdb', 'CollectionMethod')
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Flaw = apps.get_model('collections_ccdb', 'Flaw')
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ADFGPermit = apps.get_model('collections_ccdb', 'ADFGPermit')
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Collection = apps.get_model('collections_ccdb', 'Collection')
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DatasheetAttachment = apps.get_model('collections_ccdb', 'DatasheetAttachment')
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CollectionTrap = apps.get_model('collections_ccdb', 'CollectionTrap')
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for model in [CollectionTrap, Collection, Flaw, DatasheetAttachment,
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CollectionMethod, CollectionType, ADFGPermit]:
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model.objects.all().delete()
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dependencies = [
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('collections_ccdb', '0004_collections_ordering'),
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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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@ -78,7 +78,7 @@ class Collection(models.Model):
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def save(self, *args, **kwargs):
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self.display_name = "{}_{}_{}_{}".format(self.project,
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self.collection_end_date.date(), self.study_location,
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self.collection_end_date, self.study_location,
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self.collection_type)
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super(Collection, self).save(*args, **kwargs)
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@ -110,4 +110,5 @@ class CollectionTrap(models.Model):
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self.collection, self.number_of_traps, self.date_opened, self.date_closed)
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class Meta:
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unique_together = ('collection', 'date_opened', 'time_opened', 'date_closed', 'time_closed')
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unique_together = ('collection', 'date_opened', 'time_opened',
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'date_closed', 'time_closed')
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0
ccdb/collections_ccdb/tests/__init__.py
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0
ccdb/collections_ccdb/tests/__init__.py
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92
ccdb/collections_ccdb/tests/test_models.py
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92
ccdb/collections_ccdb/tests/test_models.py
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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 CollectionType, CollectionMethod, Flaw, ADFGPermit, \
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Collection, DatasheetAttachment, CollectionTrap
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from ..factories import CollectionTypeFactory, CollectionMethodFactory, \
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FlawFactory, ADFGPermitFactory, CollectionFactory, DatasheetAttachmentFactory, \
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CollectionTrapFactory
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class CollectionTypeTestCase(TestCase):
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def test_creation(self):
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c = CollectionTypeFactory()
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self.assertTrue(isinstance(c, CollectionType))
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self.assertEqual(c.__str__(), c.name)
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def test_uniqueness(self):
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c1 = CollectionTypeFactory()
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with transaction.atomic(), self.assertRaises(IntegrityError):
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CollectionTypeFactory(name=c1.name, code=c1.code)
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c3 = CollectionTypeFactory()
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self.assertTrue(isinstance(c3, CollectionType))
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class CollectionMethodTestCase(TestCase):
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def test_creation(self):
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c = CollectionMethodFactory()
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self.assertTrue(isinstance(c, CollectionMethod))
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self.assertEqual(c.__str__(), c.name)
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def test_uniqueness(self):
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c1 = CollectionMethodFactory()
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with transaction.atomic(), self.assertRaises(IntegrityError):
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CollectionMethodFactory(name=c1.name, code=c1.code)
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c3 = CollectionMethodFactory()
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self.assertTrue(isinstance(c3, CollectionMethod))
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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 ADFGPermitTestCase(TestCase):
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def test_creation(self):
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a = ADFGPermitFactory()
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self.assertTrue(isinstance(a, ADFGPermit))
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self.assertEqual(a.__str__(), a.name)
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class CollectionTestCase(TestCase):
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def test_creation(self):
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c = CollectionFactory()
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self.assertTrue(isinstance(c, Collection))
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self.assertEqual(c.__str__(), c.display_name)
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def test_uniqueness(self):
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c1 = CollectionFactory()
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with transaction.atomic(), self.assertRaises(IntegrityError):
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CollectionFactory(project=c1.project, study_location=c1.study_location,
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collection_type=c1.collection_type,
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collection_start_date=c1.collection_start_date,
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collection_end_date=c1.collection_end_date,
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collection_method=c1.collection_method)
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c3 = CollectionFactory()
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self.assertTrue(isinstance(c3, Collection))
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class DatasheetAttachmentTestCase(TestCase):
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def test_creation(self):
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d = DatasheetAttachmentFactory()
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self.assertTrue(isinstance(d, DatasheetAttachment))
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class CollectionTrapTestCase(TestCase):
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def test_creation(self):
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c = CollectionTrapFactory()
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self.assertTrue(isinstance(c, CollectionTrap))
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name = "{} # Traps: {} {} {}".format(c.collection, c.number_of_traps,
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c.date_opened, c.date_closed)
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self.assertEqual(c.__str__(), name)
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def test_uniqueness(self):
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c1 = CollectionTrapFactory()
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with transaction.atomic(), self.assertRaises(IntegrityError):
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CollectionTrapFactory(collection=c1.collection, date_opened=c1.date_opened,
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time_opened=c1.time_opened, date_closed=c1.date_closed,
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time_closed=c1.time_closed)
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c3 = CollectionTrapFactory()
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self.assertTrue(isinstance(c3, CollectionTrap))
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