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🐛 Don't assume sample_id exists, since fk is optional on BS #687

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merged 4 commits into from
Jun 4, 2024
Merged

🐛 Don't assume sample_id exists, since fk is optional on BS #687

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4b8c811
:bug: Dont assume sample_id exists, since fk is optional on BS
znatty22 Jun 4, 2024
86404cb
:sparkles: Add Biospecimen.specimen_status to target api plugin
znatty22 Jun 4, 2024
b7b98e0
:bug: Treat seq center as KF ID not string
znatty22 Jun 4, 2024
907a5d5
:rotating_light: Fix black formatting errors
znatty22 Jun 4, 2024
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2 changes: 1 addition & 1 deletion kf_lib_data_ingest/common/concept_schema.py
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Original file line number Diff line number Diff line change
Expand Up @@ -168,6 +168,7 @@ class SAMPLE(PropertyMixin):
TUMOR_DESCRIPTOR = None
EVENT_ID = None
EVENT_AGE_DAYS = None
STATUS = None

class EVENT_AGE(QuantityMixin):
pass
Expand Down Expand Up @@ -195,7 +196,6 @@ class CONCENTRATION(QuantityMixin):
CONSENT_SHORT_NAME = None

class SAMPLE_RELATIONSHIP(PropertyMixin):

class PARENT_SAMPLE(PropertyMixin):
pass

Expand Down
16 changes: 14 additions & 2 deletions kf_lib_data_ingest/target_api_plugins/kids_first_dataservice.py
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Original file line number Diff line number Diff line change
Expand Up @@ -574,7 +574,12 @@ class Biospecimen:
class_name = "biospecimen"
api_path = "biospecimens"
target_id_concept = CONCEPT.BIOSPECIMEN.TARGET_SERVICE_ID
service_id_fields = {"kf_id", "participant_id"}
service_id_fields = {
"kf_id",
"participant_id",
"sample_id",
"sequencing_center_id",
}

@classmethod
def get_key_components(cls, record, get_target_id_from_record):
Expand All @@ -589,6 +594,12 @@ def query_target_ids(cls, host, key_components):

@classmethod
def build_entity(cls, record, get_target_id_from_record):
# sample foreign key is optional
try:
sample_id = get_target_id_from_record(Sample, record)
except Exception:
sample_id = None

secondary_components = {
"kf_id": get_target_id_from_record(cls, record),
"sequencing_center_id": record.get(
Expand Down Expand Up @@ -662,6 +673,7 @@ def build_entity(cls, record, get_target_id_from_record):
record.get(CONCEPT.SAMPLE.VOLUME_UL)
or record.get(CONCEPT.BIOSPECIMEN.VOLUME_UL)
),
"specimen_status": (record.get(CONCEPT.BIOSPECIMEN.STATUS)),
"visible": record.get(CONCEPT.BIOSPECIMEN.VISIBLE),
"visibility_comment": record.get(
CONCEPT.BIOSPECIMEN.VISIBILITY_COMMENT
Expand All @@ -677,7 +689,7 @@ def build_entity(cls, record, get_target_id_from_record):
CONCEPT.BIOSPECIMEN.DBGAP_STYLE_CONSENT_CODE
),
"consent_type": record.get(CONCEPT.BIOSPECIMEN.CONSENT_SHORT_NAME),
"sample_id": get_target_id_from_record(Sample, record),
"sample_id": sample_id,
}
return {
**cls.get_key_components(record, get_target_id_from_record),
Expand Down
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