class PhenotipsAPITest(TestCase):
fixtures = ['users', '1kg_project']
@mock.patch('seqr.views.apis.phenotips_api.proxy_request',
create_proxy_request_stub())
def test_phenotips_edit(self):
url = reverse(phenotips_edit_handler,
args=['R0001_1kg', 'I000001_na19675'])
_check_login(self, url)
response = self.client.post(url,
content_type='application/json',
data=json.dumps({'some_json': 'test'}))
self.assertEqual(response.status_code, 200)
@mock.patch('seqr.views.apis.phenotips_api.proxy_request',
create_proxy_request_stub())
def test_phenotips_pdf(self):
url = reverse(phenotips_pdf_handler,
args=['R0001_1kg', 'I000001_na19675'])
_check_login(self, url)
response = self.client.post(url,
content_type='application/json',
data=json.dumps({'some_json': 'test'}))
self.assertEqual(response.status_code, 200)
class ProjectAPITest(TestCase):
fixtures = ['users', '1kg_project']
@mock.patch('seqr.views.apis.phenotips_api.proxy_request',
create_proxy_request_stub(201))
def test_create_update_and_delete_project(self):
create_project_url = reverse(create_project_handler)
_check_login(self, create_project_url)
# check validation of bad requests
response = self.client.post(create_project_url,
content_type='application/json',
data=json.dumps({'bad_json': None}))
self.assertEqual(response.status_code, 400)
response = self.client.post(create_project_url,
content_type='application/json',
data=json.dumps(
{'form': {
'missing_name': True
}}))
self.assertEqual(response.status_code, 400)
# send valid request to create project
response = self.client.post(create_project_url,
content_type='application/json',
data=json.dumps({
'name':
'new_project',
'description':
'new project description'
}))
self.assertEqual(response.status_code, 200)
# check that project was created
new_project = Project.objects.filter(name='new_project')
self.assertEqual(len(new_project), 1)
self.assertEqual(new_project[0].description, 'new project description')
# delete the project
delete_project_url = reverse(delete_project_handler,
args=[new_project[0].guid])
response = self.client.post(delete_project_url,
content_type='application/json')
self.assertEqual(response.status_code, 200)
# check that project was deleted
new_project = Project.objects.filter(name='new_project')
self.assertEqual(len(new_project), 0)
class PhenotipsAPITest(TestCase):
fixtures = ['users', '1kg_project', 'reference_data']
multi_db = True
@mock.patch('seqr.views.apis.phenotips_api.proxy_request',
create_proxy_request_stub())
def test_phenotips_edit(self):
url = reverse(phenotips_edit_handler,
args=['R0001_1kg', 'I000001_na19675'])
_check_login(self, url)
response = self.client.post(url,
content_type='application/json',
data=json.dumps({'some_json': 'test'}))
self.assertEqual(response.status_code, 200)
@mock.patch('seqr.views.apis.phenotips_api.proxy_request',
create_proxy_request_stub())
def test_phenotips_pdf(self):
url = reverse(phenotips_pdf_handler,
args=['R0001_1kg', 'I000001_na19675'])
_check_login(self, url)
response = self.client.post(url,
content_type='application/json',
data=json.dumps({'some_json': 'test'}))
self.assertEqual(response.status_code, 200)
def test_receive_hpo_table_handler(self):
url = reverse(receive_hpo_table_handler, args=['R0001_1kg'])
_check_login(self, url)
# Send invalid requests
header = 'family_id,indiv_id,hpo_term_yes,hpo_term_no'
rows = [
'1,NA19678,,',
'1,NA19679,HP:0001631 (Defect in the atrial septum),',
'1,HG00731,HP:0002017,HP:0012469 (Infantile spasms);HP:0011675 (Arrhythmia)',
]
f = SimpleUploadedFile('updates.csv',
b"{}\n{}".format(header, '\n'.join(rows)))
response = self.client.post(url, data={'f': f})
self.assertEqual(response.status_code, 400)
self.assertDictEqual(
response.json(), {
'errors': ['Invalid header, missing individual id column'],
'warnings': []
})
header = 'family_id,individual_id,hpo_term_yes,hpo_term_no'
f = SimpleUploadedFile('updates.csv',
b"{}\n{}".format(header, '\n'.join(rows)))
response = self.client.post(url, data={'f': f})
self.assertEqual(response.status_code, 400)
self.assertDictEqual(
response.json(), {
'errors': ['Invalid header, missing hpo terms columns'],
'warnings': []
})
header = 'family_id,individual_id,hpo_term_present,hpo_term_absent'
f = SimpleUploadedFile('updates.csv',
b"{}\n{}".format(header, '\n'.join(rows)))
response = self.client.post(url, data={'f': f})
self.assertEqual(response.status_code, 400)
self.assertDictEqual(
response.json(), {
'errors': [
'Unable to find individuals to update for any of the 3 parsed individuals. No matching ids found for 1 individuals. No changes detected for 2 individuals.'
],
'warnings': []
})
# send valid request
rows.append(
'1,NA19675_1,HP:0002017,HP:0012469 (Infantile spasms);HP:0011675 (Arrhythmia)'
)
f = SimpleUploadedFile('updates.csv',
b"{}\n{}".format(header, '\n'.join(rows)))
response = self.client.post(url, data={'f': f})
self.assertEqual(response.status_code, 200)
self.assertDictEqual(
response.json(), {
'updatesByIndividualGuid': {
'I000001_na19675': [
{
'id': 'HP:0002017',
'observed': 'yes',
'category': 'HP:0025031',
'label': 'Nausea and vomiting',
'type': 'phenotype'
},
{
'id': 'HP:0012469',
'observed': 'no',
'category': 'HP:0025031',
'label': 'Infantile spasms',
'type': 'phenotype'
},
]
},
'uploadedFileId':
mock.ANY,
'errors': [],
'warnings': [
"The following HPO terms were not found in seqr's HPO data and will not be added: HP:0001631 (NA19679); HP:0011675 (NA19675_1)",
'Unable to find matching ids for 1 individuals. The following entries will not be updated: HG00731',
'No changes detected for 2 individuals. The following entries will not be updated: NA19678, NA19679',
],
'info': ['1 individuals will be updated'],
})
class ProjectAPITest(TestCase):
fixtures = ['users', '1kg_project', 'reference_data']
multi_db = True
@mock.patch('seqr.views.utils.phenotips_utils.proxy_request', create_proxy_request_stub(201))
def test_create_update_and_delete_project(self):
create_project_url = reverse(create_project_handler)
_check_login(self, create_project_url)
# check validation of bad requests
response = self.client.post(create_project_url, content_type='application/json', data=json.dumps({'bad_json': None}))
self.assertEqual(response.status_code, 400)
response = self.client.post(create_project_url, content_type='application/json', data=json.dumps({'form': {'missing_name': True}}))
self.assertEqual(response.status_code, 400)
# send valid request to create project
response = self.client.post(create_project_url, content_type='application/json', data=json.dumps(
{'name': 'new_project', 'description': 'new project description', 'genomeVersion': '38'}
))
self.assertEqual(response.status_code, 200)
# check that project was created
new_project = Project.objects.filter(name='new_project')
self.assertEqual(len(new_project), 1)
self.assertEqual(new_project[0].description, 'new project description')
self.assertEqual(new_project[0].genome_version, '38')
project_guid = new_project[0].guid
self.assertSetEqual(set(response.json()['projectsByGuid'].keys()), {project_guid})
# update the project
update_project_url = reverse(update_project_handler, args=[project_guid])
response = self.client.post(update_project_url, content_type='application/json', data=json.dumps(
{'description': 'updated project description'}
))
self.assertEqual(response.status_code, 200)
self.assertEqual(response.json()['projectsByGuid'][project_guid]['description'], 'updated project description')
self.assertEqual(Project.objects.get(guid=project_guid).description, 'updated project description')
# genome version should not update
response = self.client.post(update_project_url, content_type='application/json', data=json.dumps(
{'genomeVersion': '37'}
))
self.assertEqual(response.json()['projectsByGuid'][project_guid]['genomeVersion'], '38')
self.assertEqual(Project.objects.get(guid=project_guid).genome_version, '38')
# delete the project
delete_project_url = reverse(delete_project_handler, args=[project_guid])
response = self.client.post(delete_project_url, content_type='application/json')
self.assertEqual(response.status_code, 200)
# check that project was deleted
new_project = Project.objects.filter(name='new_project')
self.assertEqual(len(new_project), 0)
@mock.patch('seqr.views.utils.orm_to_json_utils.get_objects_for_group', get_objects_for_group)
def test_project_page_data(self):
url = reverse(project_page_data, args=[PROJECT_GUID])
_check_login(self, url)
response = self.client.get(url)
self.assertEqual(response.status_code, 200)
response_json = response.json()
self.assertSetEqual(
set(response_json.keys()),
{'projectsByGuid', 'familiesByGuid', 'individualsByGuid', 'samplesByGuid', 'locusListsByGuid',
'analysisGroupsByGuid', 'genesById'}
)
self.assertSetEqual(
set(response_json['projectsByGuid'][PROJECT_GUID]['variantTagTypes'][0].keys()),
{'variantTagTypeGuid', 'name', 'category', 'description', 'color', 'order', 'numTags', 'numTagsPerFamily'}
)
self.assertSetEqual(
set(response_json['projectsByGuid'][PROJECT_GUID].keys()),
{'collaborators', 'locusListGuids', 'variantTagTypes', 'variantFunctionalTagTypes',
'detailsLoaded', 'projectGuid', 'projectCategoryGuids', 'canEdit', 'name', 'description', 'createdDate',
'lastModifiedDate', 'isPhenotipsEnabled', 'phenotipsUserId', 'genomeVersion', 'discoveryTags',
'lastAccessedDate', 'isMmeEnabled', 'mmePrimaryDataOwner', 'mmeContactInstitution', 'mmeContactUrl'}
)
self.assertEqual(
response_json['projectsByGuid'][PROJECT_GUID]['lastAccessedDate'][:10],
datetime.today().strftime('%Y-%m-%d')
)
discovery_tags = response_json['projectsByGuid'][PROJECT_GUID]['discoveryTags']
self.assertEqual(len(discovery_tags), 1)
self.assertEqual(discovery_tags[0]['variantGuid'], 'SV0000001_2103343353_r0390_100')
self.assertListEqual(response_json['genesById'].keys(), ['ENSG00000135953'])
self.assertSetEqual(
set(response_json['familiesByGuid'].values()[0].keys()),
{'projectGuid', 'familyGuid', 'individualGuids', 'analysedBy', 'pedigreeImage', 'familyId', 'displayName',
'description', 'analysisNotes', 'analysisSummary', 'causalInheritanceMode', 'analysisStatus',
'pedigreeImage', 'internalAnalysisStatus', 'internalCaseReviewNotes', 'internalCaseReviewSummary',
'createdDate', 'codedPhenotype', 'postDiscoveryOmimNumber', 'pubmedIds', 'assignedAnalyst',
'successStoryTypes', 'successStory'}
)
self.assertSetEqual(
set(response_json['individualsByGuid'].values()[0].keys()),
{'projectGuid', 'familyGuid', 'individualGuid', 'sampleGuids', 'caseReviewStatusLastModifiedBy',
'phenotipsData', 'individualId', 'paternalId', 'maternalId', 'sex', 'affected', 'displayName', 'notes',
'phenotipsPatientId', 'phenotipsData', 'createdDate', 'lastModifiedDate', 'caseReviewStatus',
'caseReviewDiscussion', 'caseReviewStatusLastModifiedDate', 'caseReviewStatusLastModifiedBy',
'paternalGuid', 'maternalGuid', 'mmeSubmittedDate', 'mmeDeletedDate', 'popPlatformFilters', 'filterFlags',
'population'}
)
self.assertSetEqual(
set(response_json['samplesByGuid'].values()[0].keys()),
{'projectGuid', 'individualGuid', 'sampleGuid', 'createdDate', 'sampleType', 'datasetType', 'sampleId',
'isActive', 'loadedDate', 'datasetFilePath', 'elasticsearchIndex'}
)
self.assertSetEqual(
set(response_json['locusListsByGuid'].values()[0].keys()),
{'locusListGuid', 'description', 'lastModifiedDate', 'numEntries', 'isPublic', 'createdBy', 'createdDate',
'canEdit', 'name'}
)
self.assertSetEqual(
set(response_json['analysisGroupsByGuid'].values()[0].keys()),
{'analysisGroupGuid', 'description', 'name', 'projectGuid', 'familyGuids'}
)
@mock.patch('seqr.views.utils.orm_to_json_utils.get_objects_for_group', get_objects_for_group)
def test_empty_project_page_data(self):
url = reverse(project_page_data, args=[EMPTY_PROJECT_GUID])
_check_login(self, url)
response = self.client.get(url)
self.assertEqual(response.status_code, 200)
response_json = response.json()
self.assertSetEqual(
set(response_json.keys()),
{'projectsByGuid', 'familiesByGuid', 'individualsByGuid', 'samplesByGuid', 'locusListsByGuid',
'analysisGroupsByGuid', 'genesById'}
)
self.assertListEqual(response_json['projectsByGuid'].keys(), [EMPTY_PROJECT_GUID])
self.assertDictEqual(response_json['familiesByGuid'], {})
self.assertDictEqual(response_json['individualsByGuid'], {})
self.assertDictEqual(response_json['samplesByGuid'], {})
self.assertDictEqual(response_json['analysisGroupsByGuid'], {})
self.assertDictEqual(response_json['genesById'], {})
def test_export_tables(self):
url = reverse(export_project_individuals_handler, args=['R0001_1kg'])
_check_login(self, url)
response = self.client.get(url + "?file_format=tsv")
self.assertEqual(response.status_code, 200)
response = self.client.get(url + "?file_format=xls")
self.assertEqual(response.status_code, 200)
class ProjectAPITest(TestCase):
fixtures = ['users', '1kg_project', 'reference_data']
multi_db = True
@mock.patch('seqr.views.utils.phenotips_utils.proxy_request',
create_proxy_request_stub(201))
def test_create_update_and_delete_project(self):
create_project_url = reverse(create_project_handler)
_check_login(self, create_project_url)
# check validation of bad requests
response = self.client.post(create_project_url,
content_type='application/json',
data=json.dumps({'bad_json': None}))
self.assertEqual(response.status_code, 400)
response = self.client.post(create_project_url,
content_type='application/json',
data=json.dumps(
{'form': {
'missing_name': True
}}))
self.assertEqual(response.status_code, 400)
# send valid request to create project
response = self.client.post(create_project_url,
content_type='application/json',
data=json.dumps({
'name': 'new_project',
'description':
'new project description',
'genomeVersion': '38'
}))
self.assertEqual(response.status_code, 200)
# check that project was created
new_project = Project.objects.filter(name='new_project')
self.assertEqual(len(new_project), 1)
self.assertEqual(new_project[0].description, 'new project description')
self.assertEqual(new_project[0].genome_version, '38')
project_guid = new_project[0].guid
self.assertSetEqual(set(response.json()['projectsByGuid'].keys()),
{project_guid})
# update the project
update_project_url = reverse(update_project_handler,
args=[project_guid])
response = self.client.post(
update_project_url,
content_type='application/json',
data=json.dumps({'description': 'updated project description'}))
self.assertEqual(response.status_code, 200)
self.assertEqual(
response.json()['projectsByGuid'][project_guid]['description'],
'updated project description')
self.assertEqual(
Project.objects.get(guid=project_guid).description,
'updated project description')
# genome version should not update
response = self.client.post(update_project_url,
content_type='application/json',
data=json.dumps({'genomeVersion': '37'}))
self.assertEqual(
response.json()['projectsByGuid'][project_guid]['genomeVersion'],
'38')
self.assertEqual(
Project.objects.get(guid=project_guid).genome_version, '38')
# delete the project
delete_project_url = reverse(delete_project_handler,
args=[project_guid])
response = self.client.post(delete_project_url,
content_type='application/json')
self.assertEqual(response.status_code, 200)
# check that project was deleted
new_project = Project.objects.filter(name='new_project')
self.assertEqual(len(new_project), 0)
def test_project_page_data(self):
url = reverse(project_page_data, args=[PROJECT_GUID])
_check_login(self, url)
response = self.client.get(url)
self.assertEqual(response.status_code, 200)
response_json = response.json()
self.assertSetEqual(
set(response_json.keys()), {
'projectsByGuid', 'familiesByGuid', 'individualsByGuid',
'samplesByGuid', 'locusListsByGuid', 'analysisGroupsByGuid',
'genesById', 'mmeSubmissionsByGuid'
})
self.assertSetEqual(
set(response_json['projectsByGuid'][PROJECT_GUID]
['variantTagTypes'][0].keys()), {
'variantTagTypeGuid', 'name', 'category', 'description',
'color', 'order', 'numTags', 'numTagsPerFamily'
})
project_fields = {
'collaborators',
'locusListGuids',
'variantTagTypes',
'variantFunctionalTagTypes',
'detailsLoaded',
'discoveryTags',
}
project_fields.update(PROJECT_FIELDS)
self.assertSetEqual(
set(response_json['projectsByGuid'][PROJECT_GUID].keys()),
project_fields)
self.assertEqual(
response_json['projectsByGuid'][PROJECT_GUID]['lastAccessedDate']
[:10],
datetime.today().strftime('%Y-%m-%d'))
discovery_tags = response_json['projectsByGuid'][PROJECT_GUID][
'discoveryTags']
self.assertEqual(len(discovery_tags), 1)
self.assertEqual(discovery_tags[0]['variantGuid'],
'SV0000001_2103343353_r0390_100')
self.assertListEqual(response_json['genesById'].keys(),
['ENSG00000135953'])
self.assertSetEqual(
set(response_json['familiesByGuid'].values()[0].keys()),
INTERNAL_FAMILY_FIELDS)
individual_fields = {'sampleGuids', 'mmeSubmissionGuid'}
individual_fields.update(INTERNAL_INDIVIDUAL_FIELDS)
self.assertSetEqual(
set(response_json['individualsByGuid'].values()[0].keys()),
individual_fields)
self.assertSetEqual(
set(response_json['samplesByGuid'].values()[0].keys()),
SAMPLE_FIELDS)
self.assertSetEqual(
set(response_json['locusListsByGuid'].values()[0].keys()),
LOCUS_LIST_FIELDS)
self.assertSetEqual(
set(response_json['analysisGroupsByGuid'].values()[0].keys()), {
'analysisGroupGuid', 'description', 'name', 'projectGuid',
'familyGuids'
})
self.assertSetEqual(
set(response_json['mmeSubmissionsByGuid'].values()[0].keys()), {
'submissionGuid', 'individualGuid', 'createdDate',
'lastModifiedDate', 'deletedDate'
})
def test_empty_project_page_data(self):
url = reverse(project_page_data, args=[EMPTY_PROJECT_GUID])
_check_login(self, url)
response = self.client.get(url)
self.assertEqual(response.status_code, 200)
response_json = response.json()
self.assertSetEqual(
set(response_json.keys()), {
'projectsByGuid', 'familiesByGuid', 'individualsByGuid',
'samplesByGuid', 'locusListsByGuid', 'analysisGroupsByGuid',
'genesById', 'mmeSubmissionsByGuid'
})
self.assertListEqual(response_json['projectsByGuid'].keys(),
[EMPTY_PROJECT_GUID])
self.assertDictEqual(response_json['familiesByGuid'], {})
self.assertDictEqual(response_json['individualsByGuid'], {})
self.assertDictEqual(response_json['samplesByGuid'], {})
self.assertDictEqual(response_json['analysisGroupsByGuid'], {})
self.assertDictEqual(response_json['genesById'], {})
self.assertDictEqual(response_json['mmeSubmissionsByGuid'], {})
self.assertDictEqual(response_json['locusListsByGuid'], {})
def test_export_tables(self):
url = reverse(export_project_individuals_handler, args=['R0001_1kg'])
_check_login(self, url)
response = self.client.get(url + "?file_format=tsv")
self.assertEqual(response.status_code, 200)
response = self.client.get(url + "?file_format=xls")
self.assertEqual(response.status_code, 200)
class ProjectAPITest(TestCase):
fixtures = ['users', '1kg_project']
@mock.patch('seqr.views.apis.phenotips_api.proxy_request',
create_proxy_request_stub(201))
def test_create_update_and_delete_project(self):
create_project_url = reverse(create_project_handler)
_check_login(self, create_project_url)
# check validation of bad requests
response = self.client.post(create_project_url,
content_type='application/json',
data=json.dumps({'bad_json': None}))
self.assertEqual(response.status_code, 400)
response = self.client.post(create_project_url,
content_type='application/json',
data=json.dumps(
{'form': {
'missing_name': True
}}))
self.assertEqual(response.status_code, 400)
# send valid request to create project
response = self.client.post(create_project_url,
content_type='application/json',
data=json.dumps({
'name': 'new_project',
'description':
'new project description',
'genomeVersion': '38'
}))
self.assertEqual(response.status_code, 200)
# check that project was created
new_project = Project.objects.filter(name='new_project')
self.assertEqual(len(new_project), 1)
self.assertEqual(new_project[0].description, 'new project description')
self.assertEqual(new_project[0].genome_version, '38')
project_guid = new_project[0].guid
self.assertSetEqual(set(response.json()['projectsByGuid'].keys()),
{project_guid})
# update the project
update_project_url = reverse(update_project_handler,
args=[project_guid])
response = self.client.post(
update_project_url,
content_type='application/json',
data=json.dumps({'description': 'updated project description'}))
self.assertEqual(response.status_code, 200)
self.assertEqual(
response.json()['projectsByGuid'][project_guid]['description'],
'updated project description')
self.assertEqual(
Project.objects.get(guid=project_guid).description,
'updated project description')
# genome version should not update
response = self.client.post(update_project_url,
content_type='application/json',
data=json.dumps({'genomeVersion': '37'}))
self.assertEqual(
response.json()['projectsByGuid'][project_guid]['genomeVersion'],
'38')
self.assertEqual(
Project.objects.get(guid=project_guid).genome_version, '38')
# delete the project
delete_project_url = reverse(delete_project_handler,
args=[project_guid])
response = self.client.post(delete_project_url,
content_type='application/json')
self.assertEqual(response.status_code, 200)
# check that project was deleted
new_project = Project.objects.filter(name='new_project')
self.assertEqual(len(new_project), 0)