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♻️ Remove study_id filter from gf target ID query #682

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♻️ Remove study_id filter from gf target ID query #682

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fe00205
:bug: Don't use default limit=100 in target ID query
znatty22 May 8, 2024
50f2b5b
:zap: Rm study_id filter for gf lookup to improve query perf
znatty22 May 8, 2024
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61 changes: 44 additions & 17 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 @@ -77,7 +77,9 @@ def get_key_components(cls, record, get_target_id_from_record):

@classmethod
def query_target_ids(cls, host, key_components):
return list(yield_kfids(host, cls.api_path, drop_none(key_components)))
filters = drop_none(key_components)
filters["limit"] = 2
return list(yield_kfids(host, cls.api_path, filters))

@classmethod
def build_entity(cls, record, get_target_id_from_record):
Expand Down Expand Up @@ -123,9 +125,9 @@ def query_target_ids(cls, host, key_components):
if kfid:
return [kfid]
else:
return list(
yield_kfids(host, cls.api_path, drop_none(key_components))
)
filters = drop_none(key_components)
filters["limit"] = 2
return list(yield_kfids(host, cls.api_path, filters))

@classmethod
def build_entity(cls, record, get_target_id_from_record):
Expand Down Expand Up @@ -168,7 +170,9 @@ def get_key_components(cls, record, get_target_id_from_record):

@classmethod
def query_target_ids(cls, host, key_components):
return list(yield_kfids(host, cls.api_path, drop_none(key_components)))
filters = drop_none(key_components)
filters["limit"] = 2
return list(yield_kfids(host, cls.api_path, filters))

@classmethod
def build_entity(cls, record, get_target_id_from_record):
Expand Down Expand Up @@ -264,7 +268,9 @@ def get_key_components(cls, record, get_target_id_from_record):

@classmethod
def query_target_ids(cls, host, key_components):
return list(yield_kfids(host, cls.api_path, drop_none(key_components)))
filters = drop_none(key_components)
filters["limit"] = 2
return list(yield_kfids(host, cls.api_path, filters))

@classmethod
def build_entity(cls, record, get_target_id_from_record):
Expand Down Expand Up @@ -325,7 +331,9 @@ def get_key_components(cls, record, get_target_id_from_record):

@classmethod
def query_target_ids(cls, host, key_components):
return list(yield_kfids(host, cls.api_path, drop_none(key_components)))
filters = drop_none(key_components)
filters["limit"] = 2
return list(yield_kfids(host, cls.api_path, filters))

@classmethod
def build_entity(cls, record, get_target_id_from_record):
Expand Down Expand Up @@ -392,6 +400,7 @@ def query_target_ids(cls, host, key_components):
# We no longer want multiple participant outcome entries.
# Patch whatever is latest for compatibility with existing dataservice
# entries.
key_components["limit"] = 2
pes = sorted(
yield_entities(host, cls.api_path, key_components),
key=lambda e: e.get("age_at_event_days", 0),
Expand Down Expand Up @@ -444,7 +453,9 @@ def get_key_components(cls, record, get_target_id_from_record):

@classmethod
def query_target_ids(cls, host, key_components):
return list(yield_kfids(host, cls.api_path, drop_none(key_components)))
filters = drop_none(key_components)
filters["limit"] = 2
return list(yield_kfids(host, cls.api_path, filters))

@classmethod
def build_entity(cls, record, get_target_id_from_record):
Expand Down Expand Up @@ -529,13 +540,15 @@ class GenomicFile:
def get_key_components(cls, record, get_target_id_from_record):
# FIXME: Temporary until KFDRC file hashes are reliably stable
return {
"study_id": get_target_id_from_record(Study, record),
# "study_id": get_target_id_from_record(Study, record),
"external_id": not_none(record[CONCEPT.GENOMIC_FILE.ID]),
}

@classmethod
def query_target_ids(cls, host, key_components):
return list(yield_kfids(host, cls.api_path, drop_none(key_components)))
filters = drop_none(key_components)
filters["limit"] = 2
return list(yield_kfids(host, cls.api_path, filters))

@classmethod
def build_entity(cls, record, get_target_id_from_record):
Expand Down Expand Up @@ -615,7 +628,9 @@ def get_key_components(cls, record, get_target_id_from_record):

@classmethod
def query_target_ids(cls, host, key_components):
return list(yield_kfids(host, cls.api_path, drop_none(key_components)))
filters = drop_none(key_components)
filters["limit"] = 2
return list(yield_kfids(host, cls.api_path, filters))

@classmethod
def build_entity(cls, record, get_target_id_from_record):
Expand Down Expand Up @@ -658,7 +673,9 @@ def get_key_components(cls, record, get_target_id_from_record):

@classmethod
def query_target_ids(cls, host, key_components):
return list(yield_kfids(host, cls.api_path, drop_none(key_components)))
filters = drop_none(key_components)
filters["limit"] = 2
return list(yield_kfids(host, cls.api_path, filters))

@classmethod
def build_entity(cls, record, get_target_id_from_record):
Expand Down Expand Up @@ -760,7 +777,9 @@ def get_key_components(cls, record, get_target_id_from_record):

@classmethod
def query_target_ids(cls, host, key_components):
return list(yield_kfids(host, cls.api_path, drop_none(key_components)))
filters = drop_none(key_components)
filters["limit"] = 2
return list(yield_kfids(host, cls.api_path, filters))

@classmethod
def build_entity(cls, record, get_target_id_from_record):
Expand Down Expand Up @@ -806,7 +825,9 @@ def get_key_components(cls, record, get_target_id_from_record):

@classmethod
def query_target_ids(cls, host, key_components):
return list(yield_kfids(host, cls.api_path, drop_none(key_components)))
filters = drop_none(key_components)
filters["limit"] = 2
return list(yield_kfids(host, cls.api_path, filters))

@classmethod
def build_entity(cls, record, get_target_id_from_record):
Expand Down Expand Up @@ -852,7 +873,9 @@ def get_key_components(cls, record, get_target_id_from_record):

@classmethod
def query_target_ids(cls, host, key_components):
return list(yield_kfids(host, cls.api_path, drop_none(key_components)))
filters = drop_none(key_components)
filters["limit"] = 2
return list(yield_kfids(host, cls.api_path, filters))

@classmethod
def build_entity(cls, record, get_target_id_from_record):
Expand Down Expand Up @@ -898,7 +921,9 @@ def get_key_components(cls, record, get_target_id_from_record):

@classmethod
def query_target_ids(cls, host, key_components):
return list(yield_kfids(host, cls.api_path, drop_none(key_components)))
filters = drop_none(key_components)
filters["limit"] = 2
return list(yield_kfids(host, cls.api_path, filters))

@classmethod
def build_entity(cls, record, get_target_id_from_record):
Expand Down Expand Up @@ -944,7 +969,9 @@ def get_key_components(cls, record, get_target_id_from_record):

@classmethod
def query_target_ids(cls, host, key_components):
return list(yield_kfids(host, cls.api_path, drop_none(key_components)))
filters = drop_none(key_components)
filters["limit"] = 2
return list(yield_kfids(host, cls.api_path, filters))

@classmethod
def build_entity(cls, record, get_target_id_from_record):
Expand Down
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