Add HTTP/SSE transport for Smithery; fix NWB Container parse error

mcp_server.py: MCP_TRANSPORT=sse env var switches to HTTP+SSE (FastMCP
SSE mode on 0.0.0.0:$PORT), enabling deployment to Railway/Render for
Smithery and other hosted MCP platforms. Default remains stdio for
Claude Desktop/Cursor local use.

ingest_linkml.py: Handle schemas where is_a references a class defined
outside the submitted file (e.g. NWB's NWBContainer → Container, which
is a PyNWB runtime base class not in nwb.yml). class_induced_slots()
now falls back to directly-declared slots on ValueError/KeyError, and
is_a is silently cleared when the parent cannot be resolved within the
schema view — build_registry_entities already handles None is_a.

Procfile + railway.toml: Railway deployment config so the MCP server
can be hosted with an HTTPS URL for Smithery registration.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EXeTeJsXisxTRXay6EoBSQ

Author: claude

Procfile

@@ -0,0 +1 @@
+web: MCP_TRANSPORT=sse PORT=$PORT python -m neuro_ghost.mcp_server

neuro_ghost/ingest_linkml.py

@@ -248,16 +248,38 @@ def parse_linkml(path: Path) -> dict[str, Any]:
     slots: dict[str, dict] = {}
 
     for cls_name in sv.all_classes():
-        cls_def       = sv.get_class(cls_name)
-        induced_slots = sv.class_induced_slots(cls_name)
+        cls_def = sv.get_class(cls_name)
+
+        try:
+            induced_slots = sv.class_induced_slots(cls_name)
+        except (ValueError, KeyError):
+            # is_a points to a class outside this schema (e.g. NWB's "Container")
+            # Fall back to directly-declared slots only.
+            induced_slots = list(cls_def.attributes.values())
+            for sname in (cls_def.slots or []):
+                try:
+                    s = sv.get_slot(sname)
+                    if s:
+                        induced_slots.append(s)
+                except Exception:
+                    pass
 
         class_uri    = cls_def.class_uri or ""
         resolved_iri = resolve_prefix(class_uri, prefixes) if class_uri else ""
 
+        # Strip is_a if the parent class isn't in this schema — build_registry_entities
+        # already handles None gracefully; leaving a dangling name would be misleading.
+        is_a = cls_def.is_a
+        if is_a:
+            try:
+                sv.get_class(is_a)
+            except (ValueError, KeyError):
+                is_a = None
+
         classes[cls_name] = {
             "iri":         resolved_iri,
             "definition":  cls_def.description or "",
-            "is_a":        cls_def.is_a,
+            "is_a":        is_a,
             "is_abstract": bool(cls_def.abstract),
             "slots":       [slot.name for slot in induced_slots],
         }

neuro_ghost/mcp_server.py

@@ -428,8 +428,18 @@ def ingest_schema(
 # ---------------------------------------------------------------------------
 
 def main() -> None:
-    """Entry point for the `neuroghost-mcp` console script."""
-    mcp.run()
+    """Entry point for the `neuroghost-mcp` console script.
+
+    Transport is selected by the MCP_TRANSPORT env var:
+      stdio (default) — for Claude Desktop / Cursor / local use
+      sse             — HTTP+SSE for Smithery and other hosted platforms
+    """
+    transport = os.environ.get("MCP_TRANSPORT", "stdio")
+    if transport == "sse":
+        port = int(os.environ.get("PORT", "8000"))
+        mcp.run(transport="sse", host="0.0.0.0", port=port)
+    else:
+        mcp.run()
 
 
 if __name__ == "__main__":

railway.toml

@@ -0,0 +1,6 @@
+[build]
+builder = "nixpacks"
+
+[deploy]
+startCommand = "MCP_TRANSPORT=sse python -m neuro_ghost.mcp_server"
+restartPolicyType = "on_failure"