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Paper test fixes #39

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Merged
Clare72 merged 3 commits into from
Apr 27, 2026
Merged

Paper test fixes #39

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003cda1
don't return NeuronsPartHere or PartsOf queries for neurons
Clare72 Apr 27, 2026
0f34292
related tools - include hierarchy tool
Clare72 Apr 27, 2026
e3b80be
stock/combo tools
Clare72 Apr 27, 2026
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74 changes: 69 additions & 5 deletions src/vfbquery/vfb_queries.py
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Original file line number Diff line number Diff line change
Expand Up @@ -291,6 +291,11 @@ class TermInfoOutputSchema(Schema):
Meta = fields.Dict(keys=fields.String(), values=fields.String(), required=True)
Tags = fields.List(fields.String(), required=True)
Queries = fields.List(QueryField(), required=False)
# RelatedTools: MCP tools (other than run_query) that are useful for this entity.
# Each entry: {"tool": "<tool_name>", "label": "...", "default_args": {...}}.
# Distinct from Queries because these are not dispatched via run_query — the
# client should call the named tool directly with default_args.
RelatedTools = fields.List(fields.Dict(), required=False)
IsIndividual = fields.Bool(missing=False, required=False)
Images = fields.Dict(keys=fields.String(), values=fields.List(fields.Nested(ImageSchema()), missing={}), required=False, allow_none=True)
IsClass = fields.Bool(missing=False, required=False)
Expand Down Expand Up @@ -400,6 +405,7 @@ def term_info_parse_object(results, short_form):
termInfo["SuperTypes"] = []
termInfo["Tags"] = []
termInfo["Queries"] = []
termInfo["RelatedTools"] = []
termInfo["IsClass"] = False
termInfo["IsIndividual"] = False
termInfo["IsTemplate"] = False
Expand Down Expand Up @@ -740,8 +746,9 @@ def term_info_parse_object(results, short_form):

# NeuronsPartHere query - for Class+Anatomy terms (synaptic neuropils, etc.)
# Matches XMI criteria: Class + Synaptic_neuropil, or other anatomical regions
if contains_all_tags(termInfo["SuperTypes"], ["Class"]) and (
"Synaptic_neuropil" in termInfo["SuperTypes"] or
# Excluded for neuron classes: "neurons with some part in <a neuron>" is not a meaningful query
if contains_all_tags(termInfo["SuperTypes"], ["Class"]) and "Neuron" not in termInfo["SuperTypes"] and (
"Synaptic_neuropil" in termInfo["SuperTypes"] or
"Anatomy" in termInfo["SuperTypes"]
):
q = NeuronsPartHere_to_schema(termInfo["Name"], {"short_form": vfbTerm.term.core.short_form})
Expand Down Expand Up @@ -783,9 +790,11 @@ def term_info_parse_object(results, short_form):
q = ComponentsOf_to_schema(termInfo["Name"], {"short_form": vfbTerm.term.core.short_form})
queries.append(q)

# PartsOf query - for any Class
# PartsOf query - for any Class except neuron classes
# Matches XMI criteria: Class (any)
if contains_all_tags(termInfo["SuperTypes"], ["Class"]):
# Excluded for neuron classes: anatomical sub-parts of a neuron type are not modelled
# in the ontology in a way that makes this query useful at the class level.
if contains_all_tags(termInfo["SuperTypes"], ["Class"]) and "Neuron" not in termInfo["SuperTypes"]:
q = PartsOf_to_schema(termInfo["Name"], {"short_form": vfbTerm.term.core.short_form})
queries.append(q)

Expand Down Expand Up @@ -941,17 +950,72 @@ def term_info_parse_object(results, short_form):
queries.append(q)
q = UpstreamClassConnectivity_to_schema(termInfo["Name"], {"short_form": vfbTerm.term.core.short_form})
queries.append(q)


# Hierarchy entries — surfaced in RelatedTools, dispatched via the
# get_hierarchy MCP tool rather than run_query.
sf_for_hier = vfbTerm.term.core.short_form
# subclass_of hierarchy is meaningful for cell-type taxonomies.
# Gate: Class + Cell (matches the "Cell"-bounded ancestor filter inside
# get_hierarchy itself).
if termInfo["SuperTypes"] and contains_all_tags(termInfo["SuperTypes"], ["Class", "Cell"]):
termInfo["RelatedTools"].append({
"tool": "get_hierarchy",
"label": f"Cell-type hierarchy of {termInfo['Name']}",
"default_args": {
"id": sf_for_hier,
"relationship": "subclass_of",
"direction": "both",
"max_depth": 1,
},
})
# part_of hierarchy is meaningful for nervous-system regions
# (brain, neuropils, ganglia, tracts), but NOT for cells/neurons or
# non-neural anatomy. Special-case the nervous system root, which lacks
# the "Nervous_system" SuperType because it isn't part_of itself.
is_ns_region = (
termInfo["SuperTypes"]
and contains_all_tags(termInfo["SuperTypes"], ["Class", "Nervous_system"])
and "Cell" not in termInfo["SuperTypes"]
)
is_ns_root = sf_for_hier == "FBbt_00005093"
if is_ns_region or is_ns_root:
termInfo["RelatedTools"].append({
"tool": "get_hierarchy",
"label": f"Region containment hierarchy of {termInfo['Name']}",
"default_args": {
"id": sf_for_hier,
"relationship": "part_of",
"direction": "both",
"max_depth": 1,
},
})

# FlyBase stock finder — for Feature terms (FBgn/FBal/FBti/FBtp/FBco/FBst)
sf = vfbTerm.term.core.short_form
if sf.startswith(("FBgn", "FBal", "FBti", "FBtp", "FBco", "FBst")):
q = FindStocks_to_schema(termInfo["Name"], {"short_form": sf})
queries.append(q)
# Also surface the dedicated find_stocks MCP tool, which exposes
# the optional collection_filter parameter (Bloomington, Kyoto,
# VDRC, etc.) that the run_query/FindStocks path does not.
termInfo["RelatedTools"].append({
"tool": "find_stocks",
"label": f"Find fly stocks for {termInfo['Name']} (with optional stock-centre filter)",
"default_args": {"feature_id": sf},
})

# FlyBase combination publications — for FBco terms
if sf.startswith("FBco"):
q = FindComboPublications_to_schema(termInfo["Name"], {"short_form": sf})
queries.append(q)
# Also surface the dedicated find_combo_publications MCP tool,
# which returns full per-publication metadata (DOI, PMID, miniref,
# year) ready for citation rendering.
termInfo["RelatedTools"].append({
"tool": "find_combo_publications",
"label": f"Find publications for {termInfo['Name']} (with full citation metadata)",
"default_args": {"fbco_id": sf},
})

# For individuals that are painted domains of anatomical regions, add parent class queries
if termInfo["IsIndividual"] and termInfo["Technique"] and any('computer' in t.lower() for t in termInfo["Technique"]):
Expand Down
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