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Local support for check samples job #4609

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merged 3 commits into from
Jan 23, 2025
+154 −107
Merged

Local support for check samples job #4609

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d4c7a5b
add local check samples test
hanars Jan 22, 2025
f659573
correctly check airtable
hanars Jan 22, 2025
707e99b
update tests
hanars Jan 22, 2025
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4 changes: 2 additions & 2 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 @@ -203,7 +203,7 @@ def _load_new_samples(cls, metadata_path, genome_version, dataset_type, run_vers
updated_project_families = []
updated_families = set()
split_project_pdos = {}
session = AirtableSession(user=None, no_auth=True)
session = AirtableSession(user=None, no_auth=True) if AirtableSession.is_airtable_enabled() else None
for project, sample_ids in samples_by_project.items():
project_sample_data = new_sample_data_by_project[project.id]
is_internal = not project_has_anvil(project) or is_internal_anvil_project(project)
Expand All @@ -215,7 +215,7 @@ def _load_new_samples(cls, metadata_path, genome_version, dataset_type, run_vers
if project_families:
updated_families.update(project_families)
updated_project_families.append((project.id, project.name, project.genome_version, project_families))
if is_internal and dataset_type == Sample.DATASET_TYPE_VARIANT_CALLS:
if session and is_internal and dataset_type == Sample.DATASET_TYPE_VARIANT_CALLS:
split_project_pdos[project.name] = cls._update_pdos(session, project.guid, sample_ids)

# Send failure notifications
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