def setUp(self):
# Create and record some data
self.result = Result.objects.all()[0]
self.pathogenicity = Pathogenicity(name='pathogenic')
self.pathogenicity.save()
self.parental_result = ParentalResult(name='heterozygous')
self.parental_result.save()
self.category = AssessmentCategory(name='other')
self.category.save()
super(AssessmentResourceTestCase, self).setUp()
def setUp(self):
super(DeleteTestCase, self).setUp()
# Immediately validates and creates a sample
management.call_command('samples', 'queue', startworkers=True)
# Create and record some data that will be used to create knowledge
# capture assessments later on.
self.pathogenicity = Pathogenicity(name='pathogenic')
self.pathogenicity.save()
self.parental_result = ParentalResult(name='heterozygous')
self.parental_result.save()
self.category = AssessmentCategory(name='other')
self.category.save()
self.user = User.objects.all()[0]
def setUp(self):
# Create and record some data
self.result = Result.objects.all()[0]
self.pathogenicity = Pathogenicity(name='pathogenic')
self.pathogenicity.save()
self.parental_result = ParentalResult(name='heterozygous')
self.parental_result.save()
self.category = AssessmentCategory(name='other')
self.category.save()
super(AssessmentResourceTestCase, self).setUp()
def setUp(self):
super(DeleteTestCase, self).setUp()
# Immediately validates and creates a sample
management.call_command('samples', 'queue',
startworkers=True)
# Create and record some data that will be used to create knowledge
# capture assessments later on.
self.pathogenicity = Pathogenicity(name='pathogenic')
self.pathogenicity.save()
self.parental_result = ParentalResult(name='heterozygous')
self.parental_result.save()
self.category = AssessmentCategory(name='other')
self.category.save()
self.user = User.objects.all()[0]
class DeleteTestCase(QueueTestCase):
def setUp(self):
super(DeleteTestCase, self).setUp()
# Immediately validates and creates a sample
management.call_command('samples', 'queue', startworkers=True)
# Create and record some data that will be used to create knowledge
# capture assessments later on.
self.pathogenicity = Pathogenicity(name='pathogenic')
self.pathogenicity.save()
self.parental_result = ParentalResult(name='heterozygous')
self.parental_result.save()
self.category = AssessmentCategory(name='other')
self.category.save()
self.user = User.objects.all()[0]
def test_delete(self):
sample_id = Sample.objects.get(batch__name='batch1', name='NA12891').id
# Associate some knowledge capture with a sample result for the sample
# we are trying to delete.
sample_result = Result.objects.filter(sample_id=sample_id)[0]
assessment = Assessment(sample_result=sample_result,
user=self.user,
assessment_category=self.category,
sanger_requested=True,
pathogenicity=self.pathogenicity,
father_result=self.parental_result,
mother_result=self.parental_result)
assessment.save()
# Since there is an assessment on the sample it should not be deleted
# by the delete-sample command.
pre_delete_sample_count = Sample.objects.count()
management.call_command('samples', 'delete-sample', sample_id)
self.assertEqual(pre_delete_sample_count, Sample.objects.count())
# Delete the assessment so that the next delete-sample command issuance
# will result in the removal of the sample and associated elements.
Assessment.objects.filter(id=assessment.id).delete()
# Get the count of all the items we expect to delete with the keys
# being the table we are deleting from the value being the count we
# expect to remove.
sample_counts = {
'cohort_sample':
CohortSample.objects.filter(set_object__id=sample_id).count(),
'sample_result':
Result.objects.filter(sample__id=sample_id).count(),
'sample_manifest':
SampleManifest.objects.filter(sample__id=sample_id).count(),
}
# Get the initial count of the tables we will be deleting from with
# the keys being the table we are deleting from and the values being
# the number of rows initially in the table before the delete command.
counts = {
'cohort_sample': CohortSample.objects.count(),
'sample_result': Result.objects.count(),
'sample_manifest': SampleManifest.objects.count(),
'sample': Sample.objects.count()
}
management.call_command('samples', 'delete-sample', sample_id)
# Make sure that all the counts after the delete match the initial
# count less the expected number of deletions.
self.assertEqual(
counts['cohort_sample'] - sample_counts['cohort_sample'],
CohortSample.objects.count())
self.assertEqual(
counts['sample_result'] - sample_counts['sample_result'],
Result.objects.count())
self.assertEqual(
counts['sample_manifest'] - sample_counts['sample_manifest'],
SampleManifest.objects.count())
self.assertEqual(counts['sample'] - 1, Sample.objects.count())
# Check the project delete method here instead of in a new test to
# prevent a reload of the data from happening.
project_id = Project.objects.all()[0].id
# Associate some knowledge capture with a sample result for a sample
# within the project we are trying to delete.
sample_result = Result.objects.filter(sample__project_id=project_id)[0]
assessment = Assessment(sample_result=sample_result,
user=self.user,
assessment_category=self.category,
sanger_requested=True,
pathogenicity=self.pathogenicity,
father_result=self.parental_result,
mother_result=self.parental_result)
assessment.save()
# Since there is an assessment on a sample in the project, the project
# and all samples in it should not be deleted by the delete-project
# command.
pre_delete_sample_count = Sample.objects.count()
pre_delete_project_count = Project.objects.count()
management.call_command('samples', 'delete-project', project_id)
self.assertEqual(pre_delete_sample_count, Sample.objects.count())
self.assertEqual(pre_delete_project_count, Project.objects.count())
# Delete the assessment so that the next delete-project command
# issuance will result in the removal of the project and associated
# elements.
Assessment.objects.filter(id=assessment.id).delete()
management.call_command('samples', 'delete-project', project_id)
# Check that deleting the project cleared out all the rest of
# the samples and their data.
self.assertEqual(0, CohortVariant.objects.count())
self.assertEqual(0, CohortSample.objects.count())
# We expect 1 cohort remaining because there is a 'World' cohort that
# is not associated with any project.
self.assertEqual(1, Cohort.objects.count())
self.assertEqual(0, Result.objects.count())
self.assertEqual(0, SampleManifest.objects.count())
self.assertEqual(0, Sample.objects.count())
self.assertEqual(0, Batch.objects.count())
self.assertEqual(0, Project.objects.count())
class DeleteTestCase(QueueTestCase):
def setUp(self):
super(DeleteTestCase, self).setUp()
# Immediately validates and creates a sample
management.call_command('samples', 'queue',
startworkers=True)
# Create and record some data that will be used to create knowledge
# capture assessments later on.
self.pathogenicity = Pathogenicity(name='pathogenic')
self.pathogenicity.save()
self.parental_result = ParentalResult(name='heterozygous')
self.parental_result.save()
self.category = AssessmentCategory(name='other')
self.category.save()
self.user = User.objects.all()[0]
def test_delete(self):
sample_id = Sample.objects.get(batch__name='batch1', name='NA12891').id
# Associate some knowledge capture with a sample result for the sample
# we are trying to delete.
sample_result = Result.objects.filter(sample_id=sample_id)[0]
assessment = Assessment(sample_result=sample_result, user=self.user,
assessment_category=self.category,
sanger_requested=True,
pathogenicity=self.pathogenicity,
father_result=self.parental_result,
mother_result=self.parental_result)
assessment.save()
# Since there is an assessment on the sample it should not be deleted
# by the delete-sample command.
pre_delete_sample_count = Sample.objects.count()
management.call_command('samples', 'delete-sample', sample_id)
self.assertEqual(pre_delete_sample_count, Sample.objects.count())
# Delete the assessment so that the next delete-sample command issuance
# will result in the removal of the sample and associated elements.
Assessment.objects.filter(id=assessment.id).delete()
# Get the count of all the items we expect to delete with the keys
# being the table we are deleting from the value being the count we
# expect to remove.
sample_counts = {
'cohort_sample':
CohortSample.objects.filter(set_object__id=sample_id).count(),
'sample_result':
Result.objects.filter(sample__id=sample_id).count(),
'sample_run':
SampleRun.objects.filter(sample__id=sample_id).count(),
'sample_manifest':
SampleManifest.objects.filter(sample__id=sample_id).count(),
}
# Get the initial count of the tables we will be deleting from with
# the keys being the table we are deleting from and the values being
# the number of rows initially in the table before the delete command.
counts = {
'cohort_sample': CohortSample.objects.count(),
'sample_result': Result.objects.count(),
'sample_run': SampleRun.objects.count(),
'sample_manifest': SampleManifest.objects.count(),
'sample': Sample.objects.count()
}
management.call_command('samples', 'delete-sample', sample_id)
# Make sure that all the counts after the delete match the initial
# count less the expected number of deletions.
self.assertEqual(
counts['cohort_sample'] - sample_counts['cohort_sample'],
CohortSample.objects.count())
self.assertEqual(
counts['sample_result'] - sample_counts['sample_result'],
Result.objects.count())
self.assertEqual(counts['sample_run'] - sample_counts['sample_run'],
SampleRun.objects.count())
self.assertEqual(
counts['sample_manifest'] - sample_counts['sample_manifest'],
SampleManifest.objects.count())
self.assertEqual(counts['sample'] - 1, Sample.objects.count())
# Check the project delete method here instead of in a new test to
# prevent a reload of the data from happening.
project_id = Project.objects.all()[0].id
# Associate some knowledge capture with a sample result for a sample
# within the project we are trying to delete.
sample_result = Result.objects.filter(sample__project_id=project_id)[0]
assessment = Assessment(sample_result=sample_result, user=self.user,
assessment_category=self.category,
sanger_requested=True,
pathogenicity=self.pathogenicity,
father_result=self.parental_result,
mother_result=self.parental_result)
assessment.save()
# Since there is an assessment on a sample in the project, the project
# and all samples in it should not be deleted by the delete-project
# command.
pre_delete_sample_count = Sample.objects.count()
pre_delete_project_count = Project.objects.count()
management.call_command('samples', 'delete-project', project_id)
self.assertEqual(pre_delete_sample_count, Sample.objects.count())
self.assertEqual(pre_delete_project_count, Project.objects.count())
# Delete the assessment so that the next delete-project command
# issuance will result in the removal of the project and associated
# elements.
Assessment.objects.filter(id=assessment.id).delete()
management.call_command('samples', 'delete-project', project_id)
# Check that deleting the project cleared out all the rest of
# the samples and their data.
self.assertEqual(0, CohortVariant.objects.count())
self.assertEqual(0, CohortSample.objects.count())
# We expect 1 cohort remaining because there is a 'World' cohort that
# is not associated with any project.
self.assertEqual(1, Cohort.objects.count())
self.assertEqual(0, Result.objects.count())
self.assertEqual(0, SampleRun.objects.count())
self.assertEqual(0, SampleManifest.objects.count())
self.assertEqual(0, Sample.objects.count())
self.assertEqual(0, Batch.objects.count())
self.assertEqual(0, Project.objects.count())
class AssessmentResourceTestCase(AuthenticatedBaseTestCase):
# TODO: Trim this test data down, it loads a lot more than is really
# necessary. All that is really needed is a single result with all the
# related data needed for that result to exist.
fixtures = ['test_data.json']
def setUp(self):
# Create and record some data
self.result = Result.objects.all()[0]
self.pathogenicity = Pathogenicity(name='pathogenic')
self.pathogenicity.save()
self.parental_result = ParentalResult(name='heterozygous')
self.parental_result.save()
self.category = AssessmentCategory(name='other')
self.category.save()
super(AssessmentResourceTestCase, self).setUp()
def test_get_empty(self):
response = self.client.get('/api/assessments/1/',
HTTP_ACCEPT='application/json')
self.assertEqual(response.status_code, codes.not_found)
response = self.client.get('/api/assessments/',
HTTP_ACCEPT='application/json')
self.assertEqual(response.status_code, codes.no_content)
def test_get(self):
assessment = Assessment(sample_result=self.result,
user=self.user,
assessment_category=self.category,
sanger_requested=True,
pathogenicity=self.pathogenicity,
father_result=self.parental_result,
mother_result=self.parental_result)
assessment.save()
response = self.client.get('/api/assessments/1/',
HTTP_ACCEPT='application/json')
self.assertEqual(response.status_code, codes.ok)
self.assertTrue(response.content)
def test_post(self):
count_before = Assessment.objects.count()
assessment_obj = {
'sample_result': self.result.id,
'user': self.user.id,
'assessment_category': self.category.id,
'pathogenicity': self.pathogenicity.id,
'father_result': self.parental_result.id,
'mother_result': self.parental_result.id,
'sanger_requested': True,
}
response = self.client.post('/api/assessments/',
data=json.dumps(assessment_obj),
content_type='application/json',
HTTP_ACCEPT='application/json')
# Post should be successful and new object should be added
self.assertEqual(response.status_code, codes.created)
self.assertEqual(Assessment.objects.count(), count_before + 1)
# Testing post with bad value
response = self.client.post('/api/assessments/',
data=json.dumps({}),
content_type='application/json',
HTTP_ACCEPT='application/json')
self.assertEqual(response.status_code, codes.unprocessable_entity)
def test_put(self):
assessment = Assessment(sample_result=self.result,
user=self.user,
assessment_category=self.category,
sanger_requested=False,
pathogenicity=self.pathogenicity,
father_result=self.parental_result,
mother_result=self.parental_result)
assessment.save()
# Create a new category to change our assessment
new_category = AssessmentCategory(name='dangerous')
new_category.save()
assessment_obj = {
'sample_result': assessment.sample_result.id,
'user': assessment.user.id,
'assessment_category': new_category.id,
'pathogenicity': assessment.pathogenicity.id,
'father_result': assessment.father_result.id,
'mother_result': assessment.mother_result.id,
'sanger_requested': assessment.sanger_requested,
}
# Try to change the assessment object's category field
response = self.client.put(
'/api/assessments/{0}/'.format(assessment.id),
data=json.dumps(assessment_obj), content_type='application/json',
HTTP_ACCEPT='application/json')
self.assertEqual(response.status_code, codes.ok)
# Confirm that the category changed
assessment = Assessment.objects.get(id=assessment.id)
self.assertEqual(assessment.assessment_category.name, 'dangerous')
# Make sure an incomplete form causes an error
response = self.client.put(
'/api/assessments/{0}/'.format(assessment.id),
data=json.dumps({'user': assessment.user.id}),
content_type='application/json',
HTTP_ACCEPT='application/json')
self.assertEqual(response.status_code, codes.unprocessable_entity)
class AssessmentResourceTestCase(AuthenticatedBaseTestCase):
# TODO: Trim this test data down, it loads a lot more than is really
# necessary. All that is really needed is a single result with all the
# related data needed for that result to exist.
fixtures = ['test_data.json']
def setUp(self):
# Create and record some data
self.result = Result.objects.all()[0]
self.pathogenicity = Pathogenicity(name='pathogenic')
self.pathogenicity.save()
self.parental_result = ParentalResult(name='heterozygous')
self.parental_result.save()
self.category = AssessmentCategory(name='other')
self.category.save()
super(AssessmentResourceTestCase, self).setUp()
def test_get_empty(self):
response = self.client.get('/api/assessments/1/',
HTTP_ACCEPT='application/json')
self.assertEqual(response.status_code, codes.not_found)
response = self.client.get('/api/assessments/',
HTTP_ACCEPT='application/json')
self.assertEqual(response.status_code, codes.no_content)
def test_get(self):
assessment = Assessment(sample_result=self.result,
user=self.user,
assessment_category=self.category,
sanger_requested=True,
pathogenicity=self.pathogenicity,
father_result=self.parental_result,
mother_result=self.parental_result)
assessment.save()
response = self.client.get('/api/assessments/1/',
HTTP_ACCEPT='application/json')
self.assertEqual(response.status_code, codes.ok)
self.assertTrue(response.content)
def test_post(self):
count_before = Assessment.objects.count()
assessment_obj = {
'sample_result': self.result.id,
'user': self.user.id,
'assessment_category': self.category.id,
'pathogenicity': self.pathogenicity.id,
'father_result': self.parental_result.id,
'mother_result': self.parental_result.id,
'sanger_requested': True,
}
response = self.client.post('/api/assessments/',
data=json.dumps(assessment_obj),
content_type='application/json',
HTTP_ACCEPT='application/json')
# Post should be successful and new object should be added
self.assertEqual(response.status_code, codes.created)
self.assertEqual(Assessment.objects.count(), count_before + 1)
# Testing post with bad value
response = self.client.post('/api/assessments/',
data=json.dumps({}),
content_type='application/json',
HTTP_ACCEPT='application/json')
self.assertEqual(response.status_code, codes.unprocessable_entity)
def test_put(self):
assessment = Assessment(sample_result=self.result,
user=self.user,
assessment_category=self.category,
sanger_requested=False,
pathogenicity=self.pathogenicity,
father_result=self.parental_result,
mother_result=self.parental_result)
assessment.save()
# Create a new category to change our assessment
new_category = AssessmentCategory(name='dangerous')
new_category.save()
assessment_obj = {
'sample_result': assessment.sample_result.id,
'user': assessment.user.id,
'assessment_category': new_category.id,
'pathogenicity': assessment.pathogenicity.id,
'father_result': assessment.father_result.id,
'mother_result': assessment.mother_result.id,
'sanger_requested': assessment.sanger_requested,
}
# Try to change the assessment object's category field
response = self.client.put('/api/assessments/{0}/'.format(
assessment.id),
data=json.dumps(assessment_obj),
content_type='application/json',
HTTP_ACCEPT='application/json')
self.assertEqual(response.status_code, codes.ok)
# Confirm that the category changed
assessment = Assessment.objects.get(id=assessment.id)
self.assertEqual(assessment.assessment_category.name, 'dangerous')
# Make sure an incomplete form causes an error
response = self.client.put(
'/api/assessments/{0}/'.format(assessment.id),
data=json.dumps({'user': assessment.user.id}),
content_type='application/json',
HTTP_ACCEPT='application/json')
self.assertEqual(response.status_code, codes.unprocessable_entity)