[jplfaria]

Why this matters in our workflow

We annotate genomes with RAST, and RAST is reached through RPCClient: RastClient uses it, and so does the
ModelSEED API. When the server returns an HTTP 500, callers should get a ServerError with the server's message.
Instead, for several common body shapes they get a TypeError raised from inside rpcclient.py. The string case has
happened in production: on 30 Jun 2026 the ModelSEED API's failure watcher logged it twice, from its RAST annotation
step (ModelSEED/modelseed-api-ops #18 and #19).

What happens

rpcclient.py L71-L79 at 062714b
does raise ServerError(**err["error"]). That works only when the error is an object whose keys are exactly
ServerError's parameters. Other shapes raise TypeError on that line:

500 response body	dev raises
{"error": "service unavailable"}	TypeError: ... argument after ** must be a mapping, not str
{"error": {"code": -32601, "message": "Method not found"}} (JSON-RPC 2.0, no name)	TypeError: ServerError.__init__() missing 1 required positional argument: 'name'
{"error": {"name": "Err", "code": 1, "message": "m", "stack": "..."}}	TypeError: ServerError.__init__() got an unexpected keyword argument 'stack'
"internal error" (a JSON string, not an object)	TypeError: string indices must be integers

How to reproduce

import modelseedpy.core.rpcclient as rc

class Resp:
    status_code = 500; ok = False; headers = {"content-type": "application/json"}
    text = '{"error": {"code": -32601, "message": "Method not found"}}'
    def json(self): return {"error": {"code": -32601, "message": "Method not found"}}

rc._requests.post = lambda *a, **k: Resp()
rc.RPCClient("http://example.invalid").call("Svc.method", [])
# dev: TypeError: ServerError.__init__() missing 1 required positional argument: 'name'

The fix

                 err = ret.json()
-                if "error" in err:
-                    raise ServerError(**err["error"])
+                error = err.get("error") if isinstance(err, dict) else None
+                if isinstance(error, dict):
+                    raise ServerError(
+                        error.get("name", "Unknown"),
+                        error.get("code", 0),
+                        error.get("message"),
+                        error.get("data"),
+                        error.get("error"),
+                    )
                 else:
                     raise ServerError("Unknown", 0, ret.text)

• An error object fills ServerError from its keys, with defaults for missing ones and extra keys ignored.
• Anything else takes the existing "Unknown" branch with the response text, as a 500 without an error key already
  does.
• A complete error object gives the same ServerError as before.
• RPCClient has one caller inside the package, RastClient (rast_client.py:57). For it, only the exception type of
  a failing call changes, from TypeError to ServerError.

Tests

This adds a new file, tests/core/test_rpcclient.py (there were no RPCClient tests). It monkeypatches
requests.post and checks:

• test_call_server_error: a complete error object keeps its name, code and message. This locks in the current
  behaviour, and it passes on dev.
• test_call_server_error_other_shapes, parametrized over the four bodies in the table: each raises a ServerError
  with the expected name, code and message.

Against dev's code, the four other-shapes cases fail and test_call_server_error passes:

E                   TypeError: ServerError.__init__() missing 1 required positional argument: 'name'
E                   TypeError: ServerError.__init__() got an unexpected keyword argument 'stack'
E                   TypeError: modelseedpy.core.rpcclient.ServerError() argument after ** must be a mapping, not str
E                   TypeError: string indices must be integers
4 failed, 1 passed

With the fix, all 5 pass. Full suite (Python 3.10, cobra 0.32.1): tests/core goes from 56 to 61 passed, and
tests/ from 58 to 63. black 22.8.0 and the other pre-commit hooks pass.

Related

• Issue: RPCClient.call raises TypeError instead of ServerError when a JSON-RPC 500 error body is not a dict jplfaria/ModelSEEDpy#13
• I sent an earlier, string-only version of this fix to cshenry/ModelSEEDpy (Numerous fixes in packages and proteome modeling #27, 98bd49f). It still raises
  TypeError for the other shapes.

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