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Enhanced Data Transfer Process with Assay File Inclusion #660

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Jan 26, 2024
Merged

Enhanced Data Transfer Process with Assay File Inclusion #660

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19 changes: 10 additions & 9 deletions scripts/create_test_subset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -276,7 +276,7 @@ def transfer_samples_sgs_assays(
type=sample_type or None,
meta=(copy_files_in_dict(s['meta'], project) or {}),
participant_id=existing_pid,
sequencing_groups=upsert_sequencing_groups(s, existing_data),
sequencing_groups=upsert_sequencing_groups(s, existing_data, project),
id=existing_sid,
)

Expand All @@ -289,7 +289,7 @@ def transfer_samples_sgs_assays(


def upsert_sequencing_groups(
sample: dict, existing_data: dict
sample: dict, existing_data: dict, project: str
) -> list[SequencingGroupUpsert]:
"""Create SG Upsert Objects for a sample"""
sgs_to_upsert: list[SequencingGroupUpsert] = []
Expand All @@ -306,7 +306,7 @@ def upsert_sequencing_groups(
technology=sg.get('technology'),
type=sg.get('type'),
assays=upsert_assays(
sg, existing_sgid, existing_data, sample.get('externalId')
sg, existing_sgid, existing_data, sample.get('externalId'), project
),
)
sgs_to_upsert.append(sg_upsert)
Expand All @@ -315,7 +315,11 @@ def upsert_sequencing_groups(


def upsert_assays(
sg: dict, existing_sgid: str | None, existing_data: dict, sample_external_id
sg: dict,
existing_sgid: str | None,
existing_data: dict,
sample_external_id,
project: str,
) -> list[AssayUpsert]:
"""Create Assay Upsert Objects for a sequencing group"""
print(sg)
Expand All @@ -325,17 +329,14 @@ def upsert_assays(
# Check if assay exists
if existing_sgid:
_existing_assay = get_existing_assay(
existing_data,
sample_external_id,
existing_sgid,
assay
existing_data, sample_external_id, existing_sgid, assay
)
existing_assay_id = _existing_assay.get('id') if _existing_assay else None
assay_upsert = AssayUpsert(
type=assay.get('type'),
id=existing_assay_id,
external_ids=assay.get('externalIds') or {},
meta=assay.get('meta'),
meta=copy_files_in_dict(assay.get('meta'), project),
)

assays_to_upsert.append(assay_upsert)
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