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A tool that disappears from tools/list and a tool that appears but rejects a call are failing at different stages. Capture what the server actually returns, compare it with what the client exposes, and then inspect the exact arguments and server-side validation. MCP schema rules, transport-specific filtering, SDK conversion, and runtime validation can all affect the result.

First, identify where the tool fails

MCP separates tool discovery from execution: the client requests tools/list, then invokes a selected tool with tools/call. That distinction narrows the diagnosis.

  • Missing from the client’s tool list: investigate discovery, client filtering, transport-specific rules, schema conversion, or name collisions.
  • Visible, but the call fails: investigate the call arguments, server-side validation, handler execution, and any protocol or connectivity errors.

Save the raw tools/list response and compare it with the tool definition shown by the host or passed to the model. For a failed invocation, save the exact tool name and arguments, the JSON-RPC response, server logs, and whether the handler was reached. The MCP tools specification defines discovery and invocation as separate operations.

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Check the schema the client actually receives

Inspect inputSchema in the transmitted tools/list response, not just the schema generator or source code. MCP requires it to be a valid JSON Schema object. If the schema omits $schema, the specification sets the default dialect to JSON Schema 2020-12.

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  • Confirm the schema is an object and that its declared types match the JSON values callers send.
  • Check that every name in required exists in properties, and that fields intended to be optional have not accidentally been marked required.
  • Verify that your test validator uses the intended dialect and inspect nested object shapes, null handling, and integer-versus-number distinctions.

For a tool with no parameters, the specification documents two object-schema forms and recommends {"type":"object","additionalProperties":false} when arguments should be explicitly empty. A standards-level validation pass is useful, but it does not prove that every client, transport, or SDK will handle the definition identically.

Look for Streamable HTTP header annotations

One documented discovery failure can look silent: with Streamable HTTP, a client must reject a tool definition if any x-mcp-header value violates the specification’s constraints. Rejection means excluding that tool from tools/list; clients should log a warning that names the tool and explains why. If a tool vanishes, inspect these annotations and the client’s logs.

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The current specification requires annotated properties to be statically reachable primitive integer, string, or boolean properties; number is not allowed. Header names must be nonempty valid HTTP field-name tokens and unique without regard to case. Integer values are also limited to the safe IEEE-754 range. These details are protocol-version-specific, so check the revision implemented by the client alongside the current MCP rules.

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Separate SDK schema conversion from server validation

Client-side conversion

A host may transform MCP schemas before making them available to a model or runtime. The OpenAI Agents SDK MCP documentation describes strict-schema conversion as best-effort: “If a schema cannot be converted, the original schema is used.” Record whether convert_schemas_to_strict is enabled, and, if instrumentation exposes it, compare the server’s schema with the one handed to the model. Do not assume a conversion failure necessarily caused the tool to disappear, because this SDK documents a fallback to the original schema.

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Server-side argument validation

A listed tool can still be rejected before its handler runs. The MCP Java SDK documentation says tool arguments are validated against inputSchema by default; on validation failure, the SDK returns a tool result marked isError with a textual error instead of invoking the handler. Check the server’s actual validator output against the exact arguments sent by the client.

Keep validation enabled while locating the mismatch. The Java SDK documents that it can be configured off, but disabling it is an SDK-specific diagnostic control, not a general fix for a disagreement between the published contract and real inputs.

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Rule out failures that are not schema errors

If discovery succeeds but execution fails or times out, schema compatibility may not be the cause. Microsoft’s MCP server troubleshooting guidance also calls out the handshake, tool list, authentication, protocol response format, concurrency, and parameter validation. Check these in the failing deployment rather than treating every failed call as a schema rejection.

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Compare working and failing deployments

When the same tool behaves differently across clients or environments, compare the points where their paths diverge:

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Compare What to inspect
Server definition vs. client-visible tool Raw tools/list response versus the host’s exposed list; check filtering and name collisions.
Schema dialect and conversion $schema, the validator’s dialect, and any host or SDK conversion settings.
Transport and annotations Transport in use, especially Streamable HTTP handling of x-mcp-header.
Arguments and server validator Exact call arguments, validation errors, and whether the handler was reached.
Post-invocation behavior Handshake, authentication, protocol response format, concurrency, and timeouts.

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