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fix!: remove temp citations ext, use reportedIn instead #239

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fix!: remove temp citations ext, use reportedIn instead #239

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12 changes: 6 additions & 6 deletions civicpy/exports/civic_gks_record.py
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Original file line number Diff line number Diff line change
Expand Up @@ -941,7 +941,12 @@ def get_reported_in(assertion: Assertion) -> list[iriReference]:
:param assertion: CIViC assertion record
:return: List of CIViC links to records which the assertion is reported in
"""
return [iriReference(f"{LINKS_URL}/assertion/{assertion.id}")]
reported_in: list[iriReference] = [
iriReference(f"{LINKS_URL}/assertion/{assertion.id}")
]
for evidence_item in assertion.evidence_items or []:
reported_in.append(iriReference(f"{LINKS_URL}/evidence/{evidence_item.id}"))
return reported_in


class CivicGksClinSigAssertion(
Expand Down Expand Up @@ -1065,7 +1070,6 @@ def get_evidence_lines(
)

evidence_items: list[CivicGksEvidence] = []
eid_links: list[str] = []
for evidence_item in assertion.evidence_items:
try:
evidence_items.append(CivicGksEvidence(evidence_item))
Expand All @@ -1081,9 +1085,6 @@ def get_evidence_lines(
evidence_item.name,
str(e),
)
finally:
# Retain all EID references
eid_links.append(f"{LINKS_URL}/evidence/{evidence_item.id}")

if assertion.assertion_type == CivicEvidenceAssertionType.PREDICTIVE:
evidence_line_cls = TherapeuticEvidenceLine
Expand All @@ -1103,7 +1104,6 @@ def get_evidence_lines(
strengthOfEvidenceProvided=MappableConcept(
primaryCoding=(Coding(code=level, system=System.AMP_ASCO_CAP))
),
extensions=[Extension(name="citations", value=eid_links)]
).root
]

Expand Down
33 changes: 12 additions & 21 deletions civicpy/tests/test_exports.py
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Original file line number Diff line number Diff line change
Expand Up @@ -482,23 +482,17 @@ def gks_aid6(
"system": "AMP/ASCO/CAP Guidelines, 2017",
},
},
"extensions": [
{
"name": "citations",
"value": [
"https://civicdb.org/links/evidence/2997",
"https://civicdb.org/links/evidence/879",
"https://civicdb.org/links/evidence/982",
"https://civicdb.org/links/evidence/883",
"https://civicdb.org/links/evidence/968",
"https://civicdb.org/links/evidence/2629"
]
}

]
}
],
"reportedIn": ["https://civicdb.org/links/assertion/6"],
"reportedIn": [
"https://civicdb.org/links/assertion/6",
"https://civicdb.org/links/evidence/2997",
"https://civicdb.org/links/evidence/879",
"https://civicdb.org/links/evidence/982",
"https://civicdb.org/links/evidence/883",
"https://civicdb.org/links/evidence/968",
"https://civicdb.org/links/evidence/2629",
],
}
return VariantClinicalSignificanceStatement(**params)

Expand Down Expand Up @@ -867,12 +861,9 @@ def test_citations(self, test_is_valid_for_gks_json, test_evidence_items, aid20)
record = CivicGksClinSigAssertion(aid20)
assert len(record.hasEvidenceLines) == 1
assert record.hasEvidenceLines[0].hasEvidenceItems is None
assert len(record.hasEvidenceLines[0].extensions) == 1
assert record.hasEvidenceLines[0].extensions[0].model_dump(
exclude_none=True
) == {
"name": "citations",
"value": ["https://civicdb.org/links/evidence/11881"],
assert {r.model_dump(exclude_none=True) for r in record.reportedIn or []} == {
"https://civicdb.org/links/evidence/11881",
"https://civicdb.org/links/assertion/20",
}


Expand Down