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SDEV-4409 - replace PHARMACOGENOMIC_SOURCE_EXCLUDE_LIST with GSC_PHAR… #6

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merged 3 commits into from
Jul 10, 2024
Merged

SDEV-4409 - replace PHARMACOGENOMIC_SOURCE_EXCLUDE_LIST with GSC_PHAR… #6

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43b35ef
SDEV-4409 - replace PHARMACOGENOMIC_SOURCE_EXCLUDE_LIST with GSC_PHAR…
dustinbleile Jul 9, 2024
76ec0f0
SDEV-4409 - GSC_PHARMACOGENOMIC_SOURCE_EXCLUDE_LIST and GSC_PHARMACOG…
dustinbleile Jul 9, 2024
e5e6987
Merge branch 'develop' into SDEV-4409_add_constants
elewis2 Jul 10, 2024
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3 changes: 2 additions & 1 deletion pori_python/graphkb/constants.py
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Original file line number Diff line number Diff line change
Expand Up @@ -66,7 +66,8 @@
CANCER_GENE = "cancer gene"
FUSION_NAMES = ["structural variant", "fusion"]

PHARMACOGENOMIC_SOURCE_EXCLUDE_LIST = ["cancer genome interpreter", "civic"]
GSC_PHARMACOGENOMIC_SOURCE_EXCLUDE_LIST = ["cancer genome interpreter", "civic"]
GSC_PHARMACOGENOMIC_SOURCE_DISPLAYNAME_EXCLUDE_LIST = ["CGI", "CIViC"]

BASE_THERAPEUTIC_TERMS = ["therapeutic efficacy", "eligibility"]
# the order here is the order these are applied, the first category matched is returned
Expand Down
17 changes: 6 additions & 11 deletions pori_python/graphkb/genes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,9 +9,9 @@
CHROMOSOMES,
FAILED_REVIEW_STATUS,
GENE_RETURN_PROPERTIES,
GSC_PHARMACOGENOMIC_SOURCE_EXCLUDE_LIST,
ONCOGENE,
ONCOKB_SOURCE_NAME,
PHARMACOGENOMIC_SOURCE_EXCLUDE_LIST,
PREFERRED_GENE_SOURCE,
RELEVANCE_BASE_TERMS,
TSO500_SOURCE_NAME,
Expand All @@ -24,10 +24,7 @@


def _get_tumourigenesis_genes_list(
conn: GraphKBConnection,
relevance: str,
sources: List[str],
ignore_cache: bool = False,
conn: GraphKBConnection, relevance: str, sources: List[str], ignore_cache: bool = False
) -> List[Ontology]:
statements = cast(
List[Statement],
Expand Down Expand Up @@ -274,12 +271,10 @@ def get_gene_linked_cancer_predisposition_info(
"evidence": {
"target": "Source",
"filters": {"@rid": get_rid(conn, "Source", "CGL")},
},
},
{
"relevance": {"target": "Vocabulary", "filters": {"@rid": relevance_rids}},
}
},
],
{"relevance": {"target": "Vocabulary", "filters": {"@rid": relevance_rids}}},
]
},
"returnProperties": [
"conditions.@class",
Expand Down Expand Up @@ -380,7 +375,7 @@ def get_gene_linked_pharmacogenomic_info(
ignore_cache=False,
):
if record["source"]: # type: ignore
if record["source"]["name"].lower() in PHARMACOGENOMIC_SOURCE_EXCLUDE_LIST: # type: ignore
if record["source"]["name"].lower() in GSC_PHARMACOGENOMIC_SOURCE_EXCLUDE_LIST: # type: ignore
continue

for condition in record["conditions"]: # type: ignore
Expand Down
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