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Inprove gregor airtable test coverage #4459

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merged 6 commits into from
Oct 31, 2024
Merged

Inprove gregor airtable test coverage #4459

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2a098fe
separate request for RNA only samples
hanars Oct 22, 2024
4aeaa7a
Merge branch 'dev' of https://github.com/broadinstitute/seqr into air…
hanars Oct 29, 2024
760bc87
update fixture
hanars Oct 29, 2024
e4905e6
clean up
hanars Oct 29, 2024
76a5bae
fix test
hanars Oct 29, 2024
50da13c
clean up
hanars Oct 29, 2024
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38 changes: 32 additions & 6 deletions seqr/views/apis/report_api_tests.py
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Original file line number Diff line number Diff line change
Expand Up @@ -67,12 +67,12 @@
},
},
{
"id": "rec2B67GmXpAkQW8z",
"id": "rec2Nkg10N1KssX1c",
"fields": {
'SeqrCollaboratorSampleID': 'NA19679',
'CollaboratorSampleID': 'NA19679',
'CollaboratorParticipantID': 'NA19679',
'SMID': 'SM-N1P91',
'SMID': 'SM-X1P92',
'Recontactable': 'Yes',
},
},
Expand All @@ -97,6 +97,16 @@
},
]}

AIRTABLE_RNA_ONLY_GREGOR_SAMPLE_RECORDS = {
"records": [
{
"id": "rec2B67GmXpAkQW8z",
"fields": {
'SMID': 'SM-N1P91',
},
},
]}

AIRTABLE_GREGOR_RECORDS = {
"records": [
{
Expand Down Expand Up @@ -793,12 +803,25 @@ def _test_gregor_export(self, url, mock_subprocess, mock_temp_dir, mock_open, mo
mock_temp_dir.return_value.__enter__.return_value = '/mock/tmp'
mock_subprocess.return_value.wait.return_value = 1

airtable_sample_url = f'{AIRTABLE_URL}/app3Y97xtbbaOopVR/Samples'
responses.add(
responses.GET, '{}/app3Y97xtbbaOopVR/Samples'.format(AIRTABLE_URL), json=AIRTABLE_GREGOR_SAMPLE_RECORDS,
status=200)
responses.GET, airtable_sample_url, json=AIRTABLE_GREGOR_SAMPLE_RECORDS, status=200, match=[
responses.matchers.query_param_matcher({'fields[]': ['CollaboratorSampleID', 'CollaboratorParticipantID', 'Recontactable', 'SMID']}, strict_match=False),
]
)
responses.add(
responses.GET, airtable_sample_url, json=AIRTABLE_GREGOR_SAMPLE_RECORDS, status=200, match=[
responses.matchers.query_param_matcher({'fields[]': ['SeqrCollaboratorSampleID', 'CollaboratorParticipantID', 'Recontactable', 'SMID']}, strict_match=False),
]
)
responses.add(
responses.GET, airtable_sample_url, json=AIRTABLE_RNA_ONLY_GREGOR_SAMPLE_RECORDS, status=200,
match=[responses.matchers.query_param_matcher({'fields[]': 'SMID'}, strict_match=False)]
)
responses.add(
responses.GET, '{}/app3Y97xtbbaOopVR/GREGoR Data Model'.format(AIRTABLE_URL), json=AIRTABLE_GREGOR_RECORDS,
status=200)

responses.add(responses.GET, MOCK_DATA_MODEL_URL, status=404)

response = self.client.post(url, content_type='application/json', data=json.dumps({}))
Expand Down Expand Up @@ -1110,7 +1133,7 @@ def _assert_expected_file(self, actual_rows, expected_rows, additional_calls=0,

def _test_expected_gregor_airtable_calls(self, additional_samples=None, additional_mondo_ids=None):
mondo_ids = ['0044970'] + (additional_mondo_ids or [])
self.assertEqual(len(responses.calls), len(mondo_ids) + 4)
self.assertEqual(len(responses.calls), len(mondo_ids) + 5)
self.assertSetEqual(
{call.request.url for call in responses.calls[:len(mondo_ids)]},
{f'https://monarchinitiative.org/v3/api/entity/MONDO:{mondo_id}' for mondo_id in mondo_ids}
Expand Down Expand Up @@ -1150,8 +1173,11 @@ def _test_expected_gregor_airtable_calls(self, additional_samples=None, addition
len(mondo_ids) + 2, "OR(CollaboratorParticipantID='NA19675',CollaboratorParticipantID='NA19679',CollaboratorParticipantID='NA20888',CollaboratorParticipantID='VCGS_FAM203_621')",
metadata_fields,
)
self.assert_expected_airtable_call(
len(mondo_ids) + 3,"OR(RECORD_ID()='rec2B67GmXpAkQW8z')",['SMID'],
)

self.assertEqual(responses.calls[len(mondo_ids) + 3].request.url, MOCK_DATA_MODEL_URL)
self.assertEqual(responses.calls[len(mondo_ids) + 4].request.url, MOCK_DATA_MODEL_URL)

def test_family_metadata(self):
url = reverse(family_metadata, args=['R0003_test'])
Expand Down
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