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edits to tests for submit.py
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@sbreiff
sbreiff committed Jul 13, 2020
1 parent 46313c2 commit 3df3aa5
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Showing 3 changed files with 34 additions and 38 deletions.
8 changes: 4 additions & 4 deletions src/encoded/submit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -110,7 +110,7 @@ def xls_to_json(xls_data, project, institution):
specimen_ids = {}
for row in rows:
indiv_alias = '{}:individual-{}'.format(project['name'], row['individual id'])
fam_alias = '{}:family-{}'.format(project['name'], row['individual id'])
fam_alias = '{}:family-{}'.format(project['name'], row['family id'])
# sp_alias = '{}:sampleproc-{}'.format(project['name'], row['specimen id'])
# create items for Individual
items = fetch_individual_metadata(row, items, indiv_alias, institution['name'])
Expand Down Expand Up @@ -192,17 +192,17 @@ def fetch_sample_metadata(row, items, indiv_alias, samp_alias, analysis_alias, f
'specimen_notes', 'research_protocol_name', 'sent_by', 'physician_id', 'indication'
]
info = map_fields(row, info, fields, 'sample')
if info['specimen_accepted'].lower() == 'y':
if info.get('specimen_accepted', '').lower() == 'y':
info['specimen_accepted'] = 'Yes'
elif info['specimen_accepted'].lower() == 'n':
elif info.get('specimen_accepted', '').lower() == 'n':
info['specimen_accepted'] = 'No'
if row.get('second specimen id'):
other_id = {'id': row['second specimen id'], 'id_type': proj_name} # add proj info?
if row.get('second specimen id type'):
other_id['id_type'] = row['second specimen id type']
info['other_specimen_ids'] = [other_id]
req_info = map_fields(row, {}, ['date sent', 'date completed'], 'requisition')
if req_info['accepted_rejected'].lower() in ['yes', 'no', 'y', 'n']:
if req_info.get('accepted_rejected', '').lower() in ['yes', 'no', 'y', 'n']:
if req_info['accepted_rejected'].lower().startswith('y'):
req_info['accepted_rejected'] = 'Accepted'
else:
Expand Down
Binary file modified src/encoded/tests/data/documents/cgap_submit_test.xlsx
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64 changes: 30 additions & 34 deletions src/encoded/tests/test_submit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@
@pytest.fixture
def row_dict():
return {
'patient id': '456',
'individual id': '456',
'family id': '333',
'sex': 'M',
'relation to proband': 'proband',
Expand All @@ -21,7 +21,10 @@ def row_dict():

@pytest.fixture
def empty_items():
return {'individual': {}, 'family': {}, 'sample': {}, 'sample_processing': {}}
return {
'individual': {}, 'family': {}, 'sample': {}, 'sample_processing': {},
'case': {}, 'report': {}, 'reports': []
}


@pytest.fixture
Expand Down Expand Up @@ -57,19 +60,19 @@ def submission_info3(submission_info2):


def test_fetch_individual_metadata_new(row_dict, empty_items):
items_out = fetch_individual_metadata(row_dict, empty_items, 'test-proj:indiv1')
items_out = fetch_individual_metadata(row_dict, empty_items, 'test-proj:indiv1', 'hms-dbmi')
assert items_out['individual']['test-proj:indiv1']['aliases'] == ['test-proj:indiv1']
assert items_out['individual']['test-proj:indiv1']['individual_id'] == '456'


def test_fetch_individual_metadata_old(row_dict):
def test_fetch_individual_metadata_old(row_dict, empty_items):
items = empty_items.copy()
items['individual'] = {'test-proj:indiv1': {
'individual_id': '456',
'age': 46,
'aliases': ['test-proj:indiv1']
}}
items_out = fetch_individual_metadata(row_dict, items, 'test-proj:indiv1')
items_out = fetch_individual_metadata(row_dict, items, 'test-proj:indiv1', 'hms-dbmi')
assert len(items['individual']) == len(items_out['individual'])
assert 'sex' in items_out['individual']['test-proj:indiv1']
assert 'age' in items_out['individual']['test-proj:indiv1']
Expand All @@ -81,7 +84,7 @@ def test_fetch_family_metadata_new(row_dict, empty_items):
assert items_out['family']['test-proj:fam1']['proband'] == 'test-proj:indiv1'


def test_fetch_family_metadata_old(row_dict):
def test_fetch_family_metadata_old(row_dict, empty_items):
items = empty_items.copy()
items['family'] = {'test-proj:fam1': {
'aliases': ['test-proj:fam1'],
Expand All @@ -95,41 +98,34 @@ def test_fetch_family_metadata_old(row_dict):
assert items_out['family']['test-proj:fam1']['mother'] == 'test-proj:indiv2'


def test_fetch_sample_metadata_sp(row_dict):
def test_fetch_sample_metadata_sp(row_dict, empty_items):
items = empty_items.copy()
items['individual'] = {'test-proj:indiv1': {}}
items_out = fetch_sample_metadata(row_dict, items, 'test-proj:indiv1', 'test-proj:samp1', 'test-proj:sp1')
items_out = fetch_sample_metadata(
row_dict, items, 'test-proj:indiv1', 'test-proj:samp1', 'test-proj:sp1', 'test-proj:fam1', 'test-proj'
)
assert items_out['sample']['test-proj:samp1']['specimen_accession'] == row_dict['specimen id']
assert items_out['sample_processing']['test-proj:sp1']['samples'] == ['test-proj:samp1']
assert items_out['individual']['test-proj:indiv1']['samples'] == ['test-proj:samp1']


def test_fetch_sample_metadata_no_sp(row_dict):
items = empty_items.copy()
items['individual'] = {'test-proj:indiv1': {}}
row_dict['report required'] = 'N'
items_out = fetch_sample_metadata(row_dict, items, 'test-proj:indiv1', 'test-proj:samp1', 'test-proj:sp1')
assert items_out['sample']['test-proj:samp1']['specimen_accession'] == row_dict['specimen id']
assert not items_out['sample_processing']


def test_create_sample_processing_groups_grp(submission_info2):
items_out = create_sample_processing_groups(submission_info2, 'test-proj:sp-multi')
assert items_out['sample_processing']['test-proj:sp-multi']['analysis_type'] == 'WGS-Group'
assert len(items_out['sample_processing']['test-proj:sp-multi']['samples']) == 2


def test_create_sample_processing_groups_one(submission_info):
items_out = create_sample_processing_groups(submission_info, 'test-proj:sp-single')
assert not items_out['sample_processing']


def test_create_sample_processing_groups_trio(submission_info3):
items_out = create_sample_processing_groups(submission_info3, 'test-proj:sp-multi')
assert items_out['sample_processing']['test-proj:sp-multi']['analysis_type'] == 'WGS-Group'
submission_info3['family']['test-proj:fam1']['father'] = 'test-proj:indiv3'
items_out = create_sample_processing_groups(submission_info3, 'test-proj:sp-multi')
assert items_out['sample_processing']['test-proj:sp-multi']['analysis_type'] == 'WGS-Trio'
# def test_create_sample_processing_groups_grp(submission_info2):
# items_out = create_sample_processing_groups(submission_info2, 'test-proj:sp-multi')
# assert items_out['sample_processing']['test-proj:sp-multi']['analysis_type'] == 'WGS-Group'
# assert len(items_out['sample_processing']['test-proj:sp-multi']['samples']) == 2
#
#
# def test_create_sample_processing_groups_one(submission_info):
# items_out = create_sample_processing_groups(submission_info, 'test-proj:sp-single')
# assert not items_out['sample_processing']
#
#
# def test_create_sample_processing_groups_trio(submission_info3):
# items_out = create_sample_processing_groups(submission_info3, 'test-proj:sp-multi')
# assert items_out['sample_processing']['test-proj:sp-multi']['analysis_type'] == 'WGS-Group'
# submission_info3['family']['test-proj:fam1']['father'] = 'test-proj:indiv3'
# items_out = create_sample_processing_groups(submission_info3, 'test-proj:sp-multi')
# assert items_out['sample_processing']['test-proj:sp-multi']['analysis_type'] == 'WGS-Trio'


def test_xls_to_json(project, institution):
Expand Down

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