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wip: get db tests to pass
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@korikuzma
korikuzma committed Nov 13, 2024
1 parent 62aee02 commit 34fe15f
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Showing 5 changed files with 87 additions and 80 deletions.
4 changes: 2 additions & 2 deletions src/metakb/database.py
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Original file line number Diff line number Diff line change
Expand Up @@ -74,15 +74,15 @@ def _get_credentials(

_CONSTRAINTS = {
"coding_constraint": "CREATE CONSTRAINT coding_constraint IF NOT EXISTS FOR (c:Coding) REQUIRE (c.code, c.label, c.system) IS UNIQUE;",
"gene_id_constraint": "CREATE CONSTRAINT gene_id_constraint IF NOT EXISTS FOR (n:Gene}) REQUIRE n.id IS UNIQUE;",
"gene_id_constraint": "CREATE CONSTRAINT gene_id_constraint IF NOT EXISTS FOR (n:Gene) REQUIRE n.id IS UNIQUE;",
"disease_id_constraint": "CREATE CONSTRAINT disease_id_constraint IF NOT EXISTS FOR (n:Disease) REQUIRE n.id IS UNIQUE;",
"therapeuticprocedure_id_constraint": "CREATE CONSTRAINT therapeuticprocedure_id_constraint IF NOT EXISTS FOR (n:TherapeuticProcedure) REQUIRE n.id IS UNIQUE;",
"variation_id_constraint": "CREATE CONSTRAINT variation_id_constraint IF NOT EXISTS FOR (n:Variation) REQUIRE n.id IS UNIQUE;",
"categoricalvariation_id_constraint": "CREATE CONSTRAINT categoricalvariation_id_constraint IF NOT EXISTS FOR (n:CategoricalVariation) REQUIRE n.id IS UNIQUE;",
"variantgroup_id_constraint": "CREATE CONSTRAINT variantgroup_id_constraint IF NOT EXISTS FOR (n:VariantGroup) REQUIRE n.id IS UNIQUE;",
"location_id_constraint": "CREATE CONSTRAINT location_id_constraint IF NOT EXISTS FOR (n:Location) REQUIRE n.id IS UNIQUE;",
"document_id_constraint": "CREATE CONSTRAINT document_id_constraint IF NOT EXISTS FOR (n:Document) REQUIRE n.id IS UNIQUE;",
"study_id_constraint": "CREATE CONSTRAINT study_id_constraint IF NOT EXISTS FOR (n:Study) REQUIRE n.id IS UNIQUE;",
"statement_id_constraint": "CREATE CONSTRAINT study_id_constraint IF NOT EXISTS FOR (n:Statement) REQUIRE n.id IS UNIQUE;",
"method_id_constraint": "CREATE CONSTRAINT method_id_constraint IF NOT EXISTS FOR (n:Method) REQUIRE n.id IS UNIQUE;",
}

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56 changes: 26 additions & 30 deletions src/metakb/load_data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ def _create_parameterized_query(
) -> str:
"""Create parameterized query string for requested params if non-null in entity.
:param entity: entity to check against, eg a Variation or Study
:param entity: entity to check against, eg a Variation or Statement
:param params: Parameter names to check
:param entity_param_prefix: Prefix for parameter names in entity object
:return: Parameterized query, such as (`name:$name`)
Expand Down Expand Up @@ -72,8 +72,10 @@ def _add_method(tx: ManagedTransaction, method: dict, ids_in_studies: set[str])
is_reported_in = method.get("reportedIn")
if is_reported_in:
# Method's documents are unique and do not currently have IDs
_add_document(tx, is_reported_in, ids_in_studies)
doc_doi = is_reported_in["doi"]
# They also only have one document
document = is_reported_in[0]
_add_document(tx, document, ids_in_studies)
doc_doi = document["doi"]
query += f"""
MERGE (d:Document {{ doi:'{doc_doi}' }})
MERGE (m) -[:IS_REPORTED_IN] -> (d)
Expand Down Expand Up @@ -278,7 +280,7 @@ def _add_categorical_variation(
_add_mappings_and_exts_to_obj(cv, mp_nonnull_keys)
mp_keys = ", ".join(mp_nonnull_keys)

defining_context = cv["definingContext"]
defining_context = cv["constraints"][0]["definingContext"]
_add_variation(tx, defining_context)
dc_type = defining_context["type"]

Expand All @@ -293,9 +295,9 @@ def _add_categorical_variation(

query = f"""
{members_match}
MERGE (dc:{dc_type}:Variation {{ id: '{defining_context['id']}' }})
MERGE (dc:Variation:{dc_type} {{ id: '{defining_context['id']}' }})
MERGE (dc) -[:HAS_LOCATION] -> (loc)
MERGE (v:{cv['type']}:CategoricalVariation {{ {mp_keys} }})
MERGE (v:Variation:{cv['type']} {{ {mp_keys} }})
MERGE (v) -[:HAS_DEFINING_CONTEXT] -> (dc)
{members_relation}
"""
Expand Down Expand Up @@ -330,7 +332,7 @@ def _add_document(
document = document_in.copy()
formatted_keys = [
_create_parameterized_query(
document, ("id", "label", "title", "pmid", "url", "doi")
document, ("id", "label", "title", "pmid", "urls", "doi")
)
]

Expand Down Expand Up @@ -366,10 +368,10 @@ def _add_obj_id_to_set(obj: dict, ids_set: set[str]) -> None:
for obj in [
study.get("specifiedBy"), # method
study.get("reportedIn"),
study.get("variant"),
study.get("therapeutic"),
study.get("tumorType"),
study.get("qualifiers", {}).get("geneContext"),
study.get("subjectVariant"),
study.get("objectTherapeutic"),
study.get("conditionQualifier"),
study.get("geneContextQualifier"),
]:
if obj:
if isinstance(obj, list):
Expand All @@ -385,7 +387,7 @@ def _add_study(tx: ManagedTransaction, study_in: dict) -> None:
"""Add study node and its relationships
:param tx: Transaction object provided to transaction functions
:param study_in: Study CDM object
:param study_in: Statement CDM object
"""
study = study_in.copy()
study_type = study["type"]
Expand All @@ -403,16 +405,14 @@ def _add_study(tx: ManagedTransaction, study_in: dict) -> None:
match_line += f"MERGE ({name} {{ id: '{ri_doc_id}'}})\n"
rel_line += f"MERGE (s) -[:IS_REPORTED_IN] -> ({name})\n"

qualifiers = study.get("qualifiers")
if qualifiers:
allele_origin = qualifiers.get("alleleOrigin")
study["alleleOrigin"] = allele_origin
match_line += "SET s.alleleOrigin=$alleleOrigin\n"
allele_origin = study.get("alleleOriginQualifier")
study["alleleOriginQualifier"] = allele_origin
match_line += "SET s.alleleOriginQualifier=$alleleOriginQualifier\n"

gene_context_id = qualifiers.get("geneContext", {}).get("id")
if gene_context_id:
match_line += f"MERGE (g:Gene {{id: '{gene_context_id}'}})\n"
rel_line += "MERGE (s) -[:HAS_GENE_CONTEXT] -> (g)\n"
gene_context_id = study.get("geneContextQualifier", {}).get("id")
if gene_context_id:
match_line += f"MERGE (g:Gene {{id: '{gene_context_id}'}})\n"
rel_line += "MERGE (s) -[:HAS_GENE_CONTEXT] -> (g)\n"

method_id = study["specifiedBy"]["id"]
match_line += f"MERGE (m {{ id: '{method_id}' }})\n"
Expand All @@ -433,24 +433,20 @@ def _add_study(tx: ManagedTransaction, study_in: dict) -> None:
match_line += f"MERGE (c:Coding {{ {coding_keys} }})\n"
rel_line += "MERGE (s) -[:HAS_STRENGTH] -> (c)\n"

variant_id = study["variant"]["id"]
if study["variant"]["type"] == "ProteinSequenceConsequence":
v_parent_type = "CategoricalVariation"
else:
v_parent_type = "Variation"
match_line += f"MERGE (v:{v_parent_type} {{ id: '{variant_id}' }})\n"
variant_id = study["subjectVariant"]["id"]
match_line += f"MERGE (v:Variation {{ id: '{variant_id}' }})\n"
rel_line += "MERGE (s) -[:HAS_VARIANT] -> (v)\n"

therapeutic_id = study["therapeutic"]["id"]
therapeutic_id = study["objectTherapeutic"]["id"]
match_line += f"MERGE (t:TherapeuticProcedure {{ id: '{therapeutic_id}' }})\n"
rel_line += "MERGE (s) -[:HAS_THERAPEUTIC] -> (t)\n"

tumor_type_id = study["tumorType"]["id"]
tumor_type_id = study["conditionQualifier"]["id"]
match_line += f"MERGE (tt:Condition {{ id: '{tumor_type_id}' }})\n"
rel_line += "MERGE (s) -[:HAS_TUMOR_TYPE] -> (tt)\n"

query = f"""
MERGE (s:{study_type}:Study {{ {study_keys} }})
MERGE (s:{study_type}:Statement {{ {study_keys} }})
{match_line}
{rel_line}
"""
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1 change: 1 addition & 0 deletions tests/conftest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -602,6 +602,7 @@ def civic_tid146():
"alternativeLabels": [
"BIBW2992",
"BIBW 2992",
"BIBW-2992",
"(2e)-N-(4-(3-Chloro-4-Fluoroanilino)-7-(((3s)-Oxolan-3-yl)Oxy)Quinoxazolin-6-yl)-4-(Dimethylamino)But-2-Enamide",
],
"extensions": [
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6 changes: 4 additions & 2 deletions tests/data/transformers/therapeutic/civic_harvester.json
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,8 @@
"aliases": [
"(2e)-N-(4-(3-Chloro-4-Fluoroanilino)-7-(((3s)-Oxolan-3-yl)Oxy)Quinoxazolin-6-yl)-4-(Dimethylamino)But-2-Enamide",
"BIBW 2992",
"BIBW2992"
"BIBW2992",
"BIBW-2992"
],
"type": "therapie"
}
Expand Down Expand Up @@ -270,7 +271,8 @@
"aliases": [
"(2e)-N-(4-(3-Chloro-4-Fluoroanilino)-7-(((3s)-Oxolan-3-yl)Oxy)Quinoxazolin-6-yl)-4-(Dimethylamino)But-2-Enamide",
"BIBW 2992",
"BIBW2992"
"BIBW2992",
"BIBW-2992"
],
"type": "therapie"
}
Expand Down
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