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♻️ Make sample its own concept and allow sample or biospecimen
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🚨 Don't mess up formmatting

🚨 Don't mess up formmatting
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@chris-s-friedman
chris-s-friedman committed May 29, 2024
1 parent 6a26596 commit 77c5cde
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Showing 2 changed files with 87 additions and 65 deletions.
35 changes: 15 additions & 20 deletions kf_lib_data_ingest/common/concept_schema.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -146,12 +146,16 @@ class EVENT_AGE(QuantityMixin):
pass

class BIOSPECIMEN_GROUP(PropertyMixin):
pass

class SAMPLE(PropertyMixin):
TISSUE_TYPE = None
NCIT_TISSUE_TYPE_ID = None
ANATOMY_SITE = None
NCIT_ANATOMY_SITE_ID = None
UBERON_ANATOMY_SITE_ID = None
COMPOSITION = None
TUMOR_DESCRIPTOR = None
EVENT_ID = None
EVENT_AGE_DAYS = None

Expand All @@ -161,36 +165,22 @@ class EVENT_AGE(QuantityMixin):
class VOLUME(QuantityMixin):
pass

SPATIAL_DESCRIPTOR = None
SHIPMENT_ORIGIN = None
SHIPMENT_DATE = None
VOLUME_UL = None
SAMPLE_PROCUREMENT = None
PRESERVATION_METHOD = None

class BIOSPECIMEN(PropertyMixin):
TISSUE_TYPE = None
NCIT_TISSUE_TYPE_ID = None
ANATOMY_SITE = None
NCIT_ANATOMY_SITE_ID = None
UBERON_ANATOMY_SITE_ID = None
TUMOR_DESCRIPTOR = None
COMPOSITION = None
EVENT_AGE_DAYS = None

class EVENT_AGE(QuantityMixin):
pass

class BIOSPECIMEN(SAMPLE):
class QUANTITY(QuantityMixin):
pass

class CONCENTRATION(QuantityMixin):
pass

SPATIAL_DESCRIPTOR = None
SHIPMENT_ORIGIN = None
SHIPMENT_DATE = None
ANALYTE = None
CONCENTRATION_MG_PER_ML = None
VOLUME_UL = None
SAMPLE_PROCUREMENT = None
DBGAP_STYLE_CONSENT_CODE = None
CONSENT_SHORT_NAME = None

Expand Down Expand Up @@ -264,14 +254,18 @@ def compile_schema():

property_path = []
property_paths = set()
_set_cls_attrs(CONCEPT, None, property_path, property_paths, include_root=False)
_set_cls_attrs(
CONCEPT, None, property_path, property_paths, include_root=False
)
return property_paths


str_to_CONCEPT = {}


def _set_cls_attrs(node, prev_node, property_path, property_paths, include_root=False):
def _set_cls_attrs(
node, prev_node, property_path, property_paths, include_root=False
):
"""
Recursive method to traverse a class hierarchy and set class attributes
equal to a string which represents a path in the hierarchy to reach the
Expand Down Expand Up @@ -355,6 +349,7 @@ class C:
CONCEPT.FAMILY_RELATIONSHIP.PERSON2,
CONCEPT.BIOSPECIMEN_GROUP,
CONCEPT.BIOSPECIMEN,
CONCEPT.SAMPLE,
CONCEPT.DIAGNOSIS,
CONCEPT.PHENOTYPE,
CONCEPT.DIAGNOSIS,
Expand Down
117 changes: 72 additions & 45 deletions kf_lib_data_ingest/target_api_plugins/kids_first_dataservice.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -398,7 +398,9 @@ def submit(cls, host, body):
class Sample:
class_name = "sample"
api_path = "samples"
target_id_concept = CONCEPT.BIOSPECIMEN_GROUP.TARGET_SERVICE_ID
target_id_concept = (
CONCEPT.SAMPLE.TARGET_SERVICE_ID or CONCEPT.BIOSPECIMEN_GROUP.TARGET_SERVICE_ID
)
service_id_fields = {"kf_id", "participant_id"}

@classmethod
Expand All @@ -416,30 +418,44 @@ def query_target_ids(cls, host, key_components):
def build_entity(cls, record, get_target_id_from_record):
secondary_components = {
"kf_id": get_target_id_from_record(cls, record),
"age_at_event_days": flexible_age(
record,
CONCEPT.BIOSPECIMEN_GROUP.EVENT_AGE_DAYS,
CONCEPT.BIOSPECIMEN_GROUP.EVENT_AGE,
"age_at_event_days": (
flexible_age(
record,
CONCEPT.SAMPLE.EVENT_AGE_DAYS,
CONCEPT.SAMPLE.EVENT_AGE,
)
or flexible_age(
record,
CONCEPT.BIOSPECIMEN.EVENT_AGE_DAYS,
CONCEPT.BIOSPECIMEN.EVENT_AGE,
)
),
"anatomical_location": record.get(CONCEPT.BIOSPECIMEN_GROUP.ANATOMY_SITE),
"method_of_sample_procurement": record.get(
CONCEPT.BIOSPECIMEN_GROUP.SAMPLE_PROCUREMENT
"anatomical_location": (
record.get(CONCEPT.SAMPLE.ANATOMY_SITE)
or record.get(CONCEPT.BIOSPECIMEN.ANATOMY_SITE)
),
"method_of_sample_procurement": (
record.get(CONCEPT.SAMPLE.SAMPLE_PROCUREMENT)
or record.get(CONCEPT.BIOSPECIMEN.SAMPLE_PROCUREMENT)
),
"participant_id": not_none(get_target_id_from_record(Participant, record)),
"preservation_method": record.get(
CONCEPT.BIOSPECIMEN_GROUP.PRESERVATION_METHOD
"preservation_method": record.get(CONCEPT.SAMPLE.PRESERVATION_METHOD),
"sample_event_key": record.get(CONCEPT.SAMPLE.EVENT_ID),
"sample_type": (
record.get(CONCEPT.SAMPLE.COMPOSITION)
or record.get(CONCEPT.BIOSPECIMEN.COMPOSITION)
),
"sample_event_key": record.get(CONCEPT.BIOSPECIMEN_GROUP.EVENT_ID),
"sample_type": record.get(CONCEPT.BIOSPECIMEN_GROUP.COMPOSITION),
"tissue_type": record.get(CONCEPT.BIOSPECIMEN_GROUP.TISSUE_TYPE),
"visible": record.get(CONCEPT.BIOSPECIMEN_GROUP.VISIBLE),
"visibility_comment": record.get(
CONCEPT.BIOSPECIMEN_GROUP.VISIBILITY_COMMENT
"tissue_type": (
record.get(CONCEPT.SAMPLE.TISSUE_TYPE)
or record.get(CONCEPT.BIOSPECIMEN.TISSUE_TYPE)
),
"visibility_reason": record.get(
CONCEPT.BIOSPECIMEN_GROUP.VISIBILTIY_REASON
"visible": record.get(CONCEPT.SAMPLE.VISIBLE),
"visibility_comment": record.get(CONCEPT.SAMPLE.VISIBILITY_COMMENT),
"visibility_reason": record.get(CONCEPT.SAMPLE.VISIBILTIY_REASON),
"volume_ul": (
record.get(CONCEPT.SAMPLE.VOLUME_UL)
or record.get(CONCEPT.BIOSPECIMEN.VOLUME_UL)
),
"volume_ul": record.get(CONCEPT.BIOSPECIMEN.VOLUME_UL),
}
return {
**cls.get_key_components(record, get_target_id_from_record),
Expand Down Expand Up @@ -473,65 +489,76 @@ def build_entity(cls, record, get_target_id_from_record):
),
"participant_id": not_none(get_target_id_from_record(Participant, record)),
"external_sample_id": (
record.get(CONCEPT.BIOSPECIMEN_GROUP.ID)
record.get(CONCEPT.SAMPLE.ID)
or record.get(CONCEPT.BIOSPECIMEN_GROUP.ID)
or not_none(record[CONCEPT.BIOSPECIMEN.ID])
),
"source_text_tissue_type": (
record.get(CONCEPT.BIOSPECIMEN.TISSUE_TYPE)
or record.get(CONCEPT.BIOSPECIMEN_GROUP.TISSUE_TYPE)
record.get(CONCEPT.SAMPLE.TISSUE_TYPE)
or record.get(CONCEPT.BIOSPECIMEN.TISSUE_TYPE)
),
"composition": (
record.get(CONCEPT.BIOSPECIMEN.COMPOSITION)
or record.get(CONCEPT.BIOSPECIMEN_GROUP.COMPOSITION)
record.get(CONCEPT.SAMPLE.COMPOSITION)
or record.get(CONCEPT.BIOSPECIMEN.COMPOSITION)
),
"source_text_anatomical_site": (
record.get(CONCEPT.BIOSPECIMEN.ANATOMY_SITE)
or record.get(CONCEPT.BIOSPECIMEN_GROUP.ANATOMY_SITE)
record.get(CONCEPT.SAMPLE.ANATOMY_SITE)
or record.get(CONCEPT.BIOSPECIMEN.ANATOMY_SITE)
),
"age_at_event_days": (
flexible_age(
record,
CONCEPT.BIOSPECIMEN.EVENT_AGE_DAYS,
CONCEPT.BIOSPECIMEN.EVENT_AGE,
CONCEPT.SAMPLE.EVENT_AGE_DAYS,
CONCEPT.SAMPLE.EVENT_AGE,
)
or flexible_age(
record,
CONCEPT.BIOSPECIMEN_GROUP.EVENT_AGE_DAYS,
CONCEPT.BIOSPECIMEN_GROUP.EVENT_AGE,
CONCEPT.BIOSPECIMEN.EVENT_AGE_DAYS,
CONCEPT.BIOSPECIMEN.EVENT_AGE,
)
),
"source_text_tumor_descriptor": record.get(
CONCEPT.BIOSPECIMEN.TUMOR_DESCRIPTOR
"source_text_tumor_descriptor": (
record.get(CONCEPT.SAMPLE.TUMOR_DESCRIPTOR)
or record.get(CONCEPT.BIOSPECIMEN.TUMOR_DESCRIPTOR)
),
"ncit_id_tissue_type": (
record.get(CONCEPT.BIOSPECIMEN.NCIT_TISSUE_TYPE_ID)
or record.get(CONCEPT.BIOSPECIMEN_GROUP.NCIT_TISSUE_TYPE_ID)
record.get(CONCEPT.SAMPLE.NCIT_TISSUE_TYPE_ID)
or record.get(CONCEPT.BIOSPECIMEN.NCIT_TISSUE_TYPE_ID)
),
"ncit_id_anatomical_site": (
record.get(CONCEPT.BIOSPECIMEN.NCIT_ANATOMY_SITE_ID)
or record.get(CONCEPT.BIOSPECIMEN_GROUP.NCIT_ANATOMY_SITE_ID)
record.get(CONCEPT.SAMPLE.NCIT_ANATOMY_SITE_ID)
or record.get(CONCEPT.BIOSPECIMEN.NCIT_ANATOMY_SITE_ID)
),
"uberon_id_anatomical_site": (
record.get(CONCEPT.BIOSPECIMEN.UBERON_ANATOMY_SITE_ID)
or record.get(CONCEPT.BIOSPECIMEN_GROUP.UBERON_ANATOMY_SITE_ID)
record.get(CONCEPT.SAMPLE.UBERON_ANATOMY_SITE_ID)
or record.get(CONCEPT.BIOSPECIMEN.UBERON_ANATOMY_SITE_ID)
),
"spatial_descriptor": (
record.get(CONCEPT.SAMPLE.SPATIAL_DESCRIPTOR)
or record.get(CONCEPT.BIOSPECIMEN.SPATIAL_DESCRIPTOR)
),
"shipment_origin": (
record.get(CONCEPT.SAMPLE.SHIPMENT_ORIGIN)
or record.get(CONCEPT.BIOSPECIMEN.SHIPMENT_ORIGIN)
),
"shipment_date": (
record.get(CONCEPT.SAMPLE.SHIPMENT_DATE)
or record.get(CONCEPT.BIOSPECIMEN.SHIPMENT_DATE)
),
"spatial_descriptor": record.get(CONCEPT.BIOSPECIMEN.SPATIAL_DESCRIPTOR),
"shipment_origin": record.get(CONCEPT.BIOSPECIMEN.SHIPMENT_ORIGIN),
"shipment_date": record.get(CONCEPT.BIOSPECIMEN.SHIPMENT_DATE),
"analyte_type": record.get(CONCEPT.BIOSPECIMEN.ANALYTE),
"concentration_mg_per_ml": record.get(
CONCEPT.BIOSPECIMEN.CONCENTRATION_MG_PER_ML
),
"volume_ul": (
record.get(CONCEPT.BIOSPECIMEN.VOLUME_UL)
or record.get(CONCEPT.BIOSPECIMEN_GROUP.VOLUME_UL)
record.get(CONCEPT.SAMPLE.VOLUME_UL)
or record.get(CONCEPT.BIOSPECIMEN.VOLUME_UL)
),
"visible": record.get(CONCEPT.BIOSPECIMEN.VISIBLE),
"visibility_comment": record.get(CONCEPT.BIOSPECIMEN.VISIBILITY_COMMENT),
"visibility_reason": record.get(CONCEPT.BIOSPECIMEN.VISIBILTIY_REASON),
"method_of_sample_procurement": (
record.get(CONCEPT.BIOSPECIMEN.SAMPLE_PROCUREMENT)
or record.get(CONCEPT.BIOSPECIMEN_GROUP.SAMPLE_PROCUREMENT)
record.get(CONCEPT.SAMPLE.SAMPLE_PROCUREMENT)
or record.get(CONCEPT.BIOSPECIMEN.SAMPLE_PROCUREMENT)
),
"dbgap_consent_code": record.get(
CONCEPT.BIOSPECIMEN.DBGAP_STYLE_CONSENT_CODE
Expand Down

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