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Also clean stray escaping in synonyms and relationship labels #80

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Merged
Robbie1977 merged 1 commit into from
Jul 16, 2026
Merged

Also clean stray escaping in synonyms and relationship labels #80

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16 changes: 14 additions & 2 deletions src/test/term_info_queries_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -29,15 +29,27 @@ def test_label_stray_backslash_cleaned(self):
"short_form": "VFB_jrchk0e3", "unique_facets": ["Adult"],
"label": "MBON01(y5β\\'2a)_L"}, "description": [], "comment": []},
"query": "Get JSON for Individual", "version": "t", "parents": [],
"relationships": [], "xrefs": [], "anatomy_channel_image": [],
"pub_syn": [], "def_pubs": []}
"relationships": [{"relation": {"iri": "i", "label": "is part\\'of",
"type": "part_of"}, "object": {"symbol": "", "iri": "i",
"types": ["Class"], "short_form": "FBbt_1", "unique_facets": [],
"label": "adult brain"}}],
"xrefs": [], "anatomy_channel_image": [],
"pub_syn": [{"synonym": {"scope": "has_exact_synonym",
"label": "MBON01(y5β\\'2a)_syn", "type": ""},
"pub": {"core": {"symbol": "", "iri": "i", "types": ["pub"],
"short_form": "Unattributed", "unique_facets": ["pub"], "label": ""},
"FlyBase": "", "PubMed": "", "DOI": ""}}], "def_pubs": []}
'''
terminfo = deserialize_term_info(terminfo_json)
# backslash stripped, apostrophe and Greek beta preserved
self.assertEqual("MBON01(y5β'2a)_L", terminfo.term.core.label)
self.assertNotIn("\\", terminfo.term.core.label)
# and it flows clean into the internal link (used for Name/Meta rendering)
self.assertNotIn("\\", terminfo.term.core.get_int_link())
# synonyms and relationship (edge) labels are cleaned too
self.assertEqual("MBON01(y5β'2a)_syn", terminfo.pub_syn[0].synonym.label)
self.assertNotIn("\\", terminfo.pub_syn[0].synonym.label)
self.assertNotIn("\\", terminfo.relationships[0].relation.label)

def test_term_info_deserialization(self):
terminfo_json = """
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8 changes: 8 additions & 0 deletions src/vfbquery/term_info_queries.py
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Expand Up @@ -133,6 +133,9 @@ class MinimalEdgeInfo:
confidence_value: Optional[str] = ""
database_cross_reference: Optional[List[str]] = None

def __post_init__(self):
self.label = clean_label(self.label)


@dataclass_json
@dataclass
Expand All @@ -141,6 +144,11 @@ class Synonym:
scope: Optional[str] = ""
type: Optional[str] = ""

def __post_init__(self):
# Synonyms carry the same over-escaping artifact as labels (e.g. a
# synonym "y5B\\'2a"); clean at ingestion so search/term-info render clean.
self.label = clean_label(self.label)

def __str__(self):
if self.scope:
return re.sub(r"([^_A-Z])([A-Z])", r"\1 \2", self.scope).replace("has ", "") + ": " + self.label
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