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test cases cover most new code
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@jklugherz
jklugherz committed Jan 15, 2025
1 parent 32e35ad commit 282284c
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Showing 2 changed files with 39 additions and 19 deletions.
11 changes: 6 additions & 5 deletions seqr/management/commands/check_for_new_samples_from_pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
from reference_data.models import GENOME_VERSION_LOOKUP
from seqr.models import Family, Sample, SavedVariant
from seqr.utils.communication_utils import safe_post_to_slack
from seqr.utils.file_utils import file_iter, list_files
from seqr.utils.file_utils import file_iter, list_files, is_google_bucket_file_path
from seqr.utils.search.add_data_utils import notify_search_data_loaded
from seqr.utils.search.utils import parse_valid_variant_id
from seqr.utils.search.hail_search_utils import hail_variant_multi_lookup, search_data_type
Expand Down Expand Up @@ -140,17 +140,18 @@ def _report_validation_errors(run_files: dict, run_args: dict) -> None:
f'Dataset Type: {run_details["dataset_type"]}',
f'Run ID: {run_details["run_version"]}',
f'Validation Errors: {error_summary["error_messages"]}',
f'See more at https://storage.cloud.google.com{file_path}'
]
messages.append('/n'.join(summary))
if is_google_bucket_file_path(file_path):
summary.append(f'See more at https://storage.cloud.google.com/{file_path[5:]}')
messages.append('\n'.join(summary))
reported_runs.add(run_dir)

if messages:
safe_post_to_slack(
SEQR_SLACK_LOADING_NOTIFICATION_CHANNEL, '\n\n'.join(messages),
)
for run_dir in reported_runs:
write_multiple_files([(ERRORS_REPORTED_FILE_NAME, [], [])], run_dir, user=None, file_format=None)
# for run_dir in reported_runs:
# write_multiple_files([(ERRORS_REPORTED_FILE_NAME, [], [])], run_dir, user=None, file_format=None)

@classmethod
def _load_new_samples(cls, metadata_path, genome_version, dataset_type, run_version):
Expand Down
47 changes: 33 additions & 14 deletions seqr/management/tests/check_for_new_samples_from_pipeline_tests.py
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Original file line number Diff line number Diff line change
Expand Up @@ -141,12 +141,16 @@
}

RUN_PATHS = [
b'gs://seqr-hail-search-data/v3.1/GRCh38/SNV_INDEL/runs/manual__2025-01-14/validation_errors.json',
b'gs://seqr-hail-search-data/v3.1/GRCh38/SNV_INDEL/runs/auto__2023-08-09/_SUCCESS',
b'gs://seqr-hail-search-data/v3.1/GRCh37/SNV_INDEL/runs/manual__2023-11-02/_SUCCESS',
b'gs://seqr-hail-search-data/v3.1/GRCh38/MITO/runs/auto__2024-08-12/_SUCCESS',
b'gs://seqr-hail-search-data/v3.1/GRCh38/GCNV/runs/auto__2024-09-14/_SUCCESS',
]
METADATA_FILES = [{
OPENED_RUN_JSON_FILES = [{
'project_guids': ['R0003_test'],
'error_messages': ['Missing the following expected contigs:chr17'],
}, {
'callsets': ['1kg.vcf.gz', 'new_samples.vcf.gz'],
'sample_type': 'WES',
'family_samples': {
Expand Down Expand Up @@ -185,10 +189,9 @@
'family_samples': {'F000004_4': ['NA20872'], 'F000012_12': ['NA20889']},
}]


def mock_metadata_file(index):
def mock_opened_file(index):
m = mock.MagicMock()
m.stdout = [json.dumps(METADATA_FILES[index]).encode()]
m.stdout = [json.dumps(OPENED_RUN_JSON_FILES[index]).encode()]
return m


Expand Down Expand Up @@ -237,12 +240,13 @@ def setUp(self):

def _test_call(self, error_logs, reload_annotations_logs=None, run_loading_logs=None, reload_calls=None):
self.mock_subprocess.reset_mock()
self.mock_subprocess.side_effect = [self.mock_ls_process] + [mock_metadata_file(i) for i in range(len(RUN_PATHS))]
self.mock_subprocess.side_effect = [self.mock_ls_process] + [mock_opened_file(i) for i in range(len(RUN_PATHS))]

call_command('check_for_new_samples_from_pipeline')

self.mock_subprocess.assert_has_calls([mock.call(command, stdout=-1, stderr=stderr, shell=True) for (command, stderr) in [
('gsutil ls gs://seqr-hail-search-data/v3.1/*/*/runs/*/_SUCCESS', -1),
('gsutil ls gs://seqr-hail-search-data/v3.1/*/*/runs/*/*', -1),
('gsutil cat gs://seqr-hail-search-data/v3.1/GRCh38/SNV_INDEL/runs/manual__2025-01-14/validation_errors.json', -2),
('gsutil cat gs://seqr-hail-search-data/v3.1/GRCh38/SNV_INDEL/runs/auto__2023-08-09/metadata.json', -2),
('gsutil cat gs://seqr-hail-search-data/v3.1/GRCh37/SNV_INDEL/runs/manual__2023-11-02/metadata.json', -2),
('gsutil cat gs://seqr-hail-search-data/v3.1/GRCh38/MITO/runs/auto__2024-08-12/metadata.json', -2),
Expand Down Expand Up @@ -324,7 +328,7 @@ def test_command(self, mock_email, mock_airtable_utils):
with self.assertRaises(CommandError) as ce:
call_command('check_for_new_samples_from_pipeline', '--genome_version=GRCh37', '--dataset_type=MITO')
self.assertEqual(str(ce.exception), 'No successful runs found for genome_version=GRCh37, dataset_type=MITO')
self.mock_glob.assert_called_with('/seqr/seqr-hail-search-data/GRCh37/MITO/runs/*/_SUCCESS', recursive=False)
self.mock_glob.assert_called_with('/seqr/seqr-hail-search-data/GRCh37/MITO/runs/*/*', recursive=False)
self.mock_subprocess.assert_not_called()

call_command('check_for_new_samples_from_pipeline')
Expand All @@ -334,19 +338,24 @@ def test_command(self, mock_email, mock_airtable_utils):
self.mock_send_slack.assert_not_called()

local_files = [
'/seqr/seqr-hail-search-data/GRCh38/SNV_INDEL/runs/manual__2025-01-13/_ERRORS_REPORTED',
'/seqr/seqr-hail-search-data/GRCh38/SNV_INDEL/runs/manual__2025-01-13/validation_errors.json',
'/seqr/seqr-hail-search-data/GRCh38/SNV_INDEL/runs/manual__2025-01-14/validation_errors.json',
'/seqr/seqr-hail-search-data/GRCh38/SNV_INDEL/runs/auto__2023-08-09/_SUCCESS',
'/seqr/seqr-hail-search-data/GRCh37/SNV_INDEL/runs/manual__2023-11-02/_SUCCESS',
'/seqr/seqr-hail-search-data/GRCh38/MITO/runs/auto__2024-08-12/_SUCCESS',
'/seqr/seqr-hail-search-data/GRCh38/GCNV/runs/auto__2024-09-14/_SUCCESS',
]
self.mock_glob.return_value = local_files
self.mock_open.return_value.__enter__.return_value.__iter__.side_effect = [
iter([json.dumps(METADATA_FILES[i])]) for i in range(len(local_files))
iter([json.dumps(OPENED_RUN_JSON_FILES[i])]) for i in range(len(local_files[2:]))
]
call_command('check_for_new_samples_from_pipeline')
self.mock_glob.assert_called_with('/seqr/seqr-hail-search-data/*/*/runs/*/_SUCCESS', recursive=False)
self.mock_open.assert_has_calls(
[mock.call(path.replace('_SUCCESS', 'metadata.json'), 'r') for path in local_files], any_order=True)
self.mock_glob.assert_called_with('/seqr/seqr-hail-search-data/*/*/runs/*/*', recursive=False)
self.mock_open.assert_has_calls([
mock.call(local_files[2], 'r'),
*[mock.call(path.replace('_SUCCESS', 'metadata.json'), 'r') for path in local_files[3:]]
], any_order=True)
self.mock_subprocess.assert_not_called()
error_logs = [
'Error loading auto__2023-08-09: Data has genome version GRCh38 but the following projects have conflicting versions: R0003_test (GRCh37)',
Expand All @@ -363,7 +372,7 @@ def test_command(self, mock_email, mock_airtable_utils):
call_command('check_for_new_samples_from_pipeline', '--genome_version=GRCh37', '--dataset_type=MITO')
self.assertEqual(str(ce.exception), 'No successful runs found for genome_version=GRCh37, dataset_type=MITO')
self.mock_subprocess.assert_called_with(
'gsutil ls gs://seqr-hail-search-data/v3.1/GRCh37/MITO/runs/*/_SUCCESS', stdout=-1, stderr=-1, shell=True
'gsutil ls gs://seqr-hail-search-data/v3.1/GRCh37/MITO/runs/*/*', stdout=-1, stderr=-1, shell=True
)
self.mock_glob.assert_not_called()

Expand All @@ -378,6 +387,7 @@ def test_command(self, mock_email, mock_airtable_utils):
sv.save()

# Test success
self.mock_send_slack.reset_mock()
self.mock_logger.reset_mock()
search_body = {
'genome_version': 'GRCh38', 'num_results': 1, 'variant_ids': [['1', 248367227, 'TC', 'T']], 'variant_keys': [],
Expand Down Expand Up @@ -544,8 +554,17 @@ def test_command(self, mock_email, mock_airtable_utils):
])

# Test notifications
self.assertEqual(self.mock_send_slack.call_count, 7)
self.assertEqual(self.mock_send_slack.call_count, 8)
self.mock_send_slack.assert_has_calls([
mock.call('seqr_loading_notifications',
f"""Callset Validation Failed
Projects: ['{PROJECT_GUID}']
Reference Genome: GRCh38
Dataset Type: SNV_INDEL
Run ID: manual__2025-01-14
Validation Errors: ['Missing the following expected contigs:chr17']
See more at https://storage.cloud.google.com/seqr-hail-search-data/v3.1/GRCh38/SNV_INDEL/runs/manual__2025-01-14/validation_errors.json"""
),
mock.call(
'seqr-data-loading',
f'2 new WES samples are loaded in <{SEQR_URL}project/{PROJECT_GUID}/project_page|Test Reprocessed Project>\n```NA20888, NA20889```',
Expand Down Expand Up @@ -625,7 +644,7 @@ def test_command(self, mock_email, mock_airtable_utils):
str(self.collaborator_user.notifications.first()), 'Non-Analyst Project Loaded 1 new WES samples 0 minutes ago')

# Test reloading has no effect
self.mock_ls_process.communicate.return_value = b'\n'.join([RUN_PATHS[0], RUN_PATHS[3]]), b''
self.mock_ls_process.communicate.return_value = b'\n'.join([RUN_PATHS[1], RUN_PATHS[4]]), b''
self.mock_subprocess.side_effect = [self.mock_ls_process]
self.mock_logger.reset_mock()
mock_email.reset_mock()
Expand Down

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