Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update PDO status for failed sex/relatedness PDOs #4630

Merged
merged 1 commit into from
Jan 29, 2025
Merged

Update PDO status for failed sex/relatedness PDOs #4630

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions seqr/management/commands/check_for_new_samples_from_pipeline.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
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
from seqr.views.utils.airtable_utils import AirtableSession, LOADABLE_PDO_STATUSES, AVAILABLE_PDO_STATUS, LOADING_PDO_STATUS
from seqr.views.utils.airtable_utils import AirtableSession, LOADABLE_PDO_STATUSES, AVAILABLE_PDO_STATUS
from seqr.views.utils.dataset_utils import match_and_update_search_samples
from seqr.views.utils.export_utils import write_multiple_files
from seqr.views.utils.permissions_utils import is_internal_anvil_project, project_has_anvil
Expand Down Expand Up @@ -298,7 +298,7 @@ def _update_pdos(session, project_guid, sample_ids):
# Create PDOs and then update Samples with new PDOs
# Does not create PDOs with Samples directly as that would not remove Samples from old PDOs
new_pdos = session.safe_create_records('PDO', [
{'PDO': pdo_name, **pdo, 'PDOStatus': LOADING_PDO_STATUS} for pdo_name, (_, pdo) in pdos_to_create.items()
{'PDO': pdo_name, **pdo, 'PDOStatus': 'PM team (Relatedness checks)'} for pdo_name, (_, pdo) in pdos_to_create.items()
])
pdo_id_map = {pdos_to_create[record['fields']['PDO']][0]: record['id'] for record in new_pdos}
for pdo_id, sample_record_ids in skipped_pdo_samples.items():
Expand Down
2 changes: 1 addition & 1 deletion seqr/management/tests/check_for_new_samples_from_pipeline_tests.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -774,7 +774,7 @@ def _assert_expected_airtable_calls(self):
self.assertDictEqual(json.loads(create_pdos_request.body), {'records': [{'fields': {
'PDO': 'PDO-1234_sr',
'SeqrProjectURL': 'https://test-seqr.org/project/R0003_test/project_page',
'PDOStatus': 'Methods (Loading)',
'PDOStatus': 'PM team (Relatedness checks)',
'PDOName': 'RGP_WGS_12',
}}]})
update_samples_request = responses.calls[4].request
Expand Down
Loading