codeocean-mcp-server 0.7.0__tar.gz → 0.7.2__tar.gz

{codeocean_mcp_server-0.7.0 → codeocean_mcp_server-0.7.2}/CHANGELOG.md

@@ -1,7 +1,16 @@
 CHANGELOG
 =========
 
-## 0.7.0 (2025-10-21)
+## 0.7.2 (2025-12-27)
+
+- [#20](https://github.com/codeocean/codeocean-mcp-server/pull/20) feat: custom log formatting
+
+## 0.7.1 (2024-12-23)
+
+- [#18](https://github.com/codeocean/codeocean-mcp-server/pull/18) chore: ruff format and dep update
+- [#17](https://github.com/codeocean/codeocean-mcp-server/pull/17) fix: Handle dataclasses.MISSING properly in dataclass_to_pydantic
+
+## 0.7.0 (2024-10-21)
 
 - [#15](https://github.com/codeocean/codeocean-mcp-server/pull/15) feat: update codeocean sdk and search_pipelines tool
 

{codeocean_mcp_server-0.7.0 → codeocean_mcp_server-0.7.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: codeocean-mcp-server
-Version: 0.7.0
+Version: 0.7.2
 Summary: Code Ocean MCP Server
 Project-URL: Homepage, https://github.com/codeocean/codeocean-mcp-server
 Project-URL: Issues, https://github.com/codeocean/codeocean-mcp-server/issues
@@ -228,3 +228,9 @@ This will start a web server where you can:
 - View available tools and resources
 - Test tool calls interactively
 - See server logs and responses
+
+## Log Formatting (Optional)
+
+The MCP server supports custom log formatting through the `LOG_FORMAT` environment variable. This allows you to control the format of log messages output by the server.
+**Example Format Strings:** `"%(asctime)s %(levelname)s [%(name)s] %(message)s"`.
+If `LOG_FORMAT` is not set, the server uses FastMCP's default logging configuration.

{codeocean_mcp_server-0.7.0 → codeocean_mcp_server-0.7.2}/README.md

@@ -210,3 +210,9 @@ This will start a web server where you can:
 - View available tools and resources
 - Test tool calls interactively
 - See server logs and responses
+
+## Log Formatting (Optional)
+
+The MCP server supports custom log formatting through the `LOG_FORMAT` environment variable. This allows you to control the format of log messages output by the server.
+**Example Format Strings:** `"%(asctime)s %(levelname)s [%(name)s] %(message)s"`.
+If `LOG_FORMAT` is not set, the server uses FastMCP's default logging configuration.

{codeocean_mcp_server-0.7.0 → codeocean_mcp_server-0.7.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "codeocean-mcp-server"
-version = "0.7.0"
+version = "0.7.2"
 authors = [{ name = "Code Ocean", email = "dev@codeocean.com" }]
 description = "Code Ocean MCP Server"
 readme = "README.md"
@@ -18,12 +18,12 @@ license = "MIT"
 
 [dependency-groups]
 dev = [
-  "boto3>=1.39.0",
-  "deepdiff>=8.5.0",
-  "hatch>=1.14.1",
+  "boto3>=1.42.17",
+  "deepdiff>=8.6.1",
+  "hatch>=1.16.2",
   "mcp-python-client>=0.1.9",
-  "pytest>=8.4.1",
-  "ruff>=0.12.1",
+  "pytest>=9.0.2",
+  "ruff>=0.14.10",
 ]
 
 [project.urls]
@@ -58,7 +58,8 @@ line-length = 120
 
 [tool.ruff.lint]
 select = ["C", "D", "E", "F", "I", "W"]
-ignore = ["D100", "D104"]
+ignore = ["D100", "D104", "D203", "D213"]
+
 
 [tool.pytest.ini_options]
 filterwarnings = [

codeocean_mcp_server-0.7.2/src/codeocean_mcp_server/logging_config.py

@@ -0,0 +1,47 @@
+import logging
+import os
+import sys
+
+
+def configure_logging() -> None:
+    """Configure logging based on LOG_FORMAT environment variable.
+
+    If LOG_FORMAT is set, configures the root logger with a StreamHandler
+    using the specified format string. This must be called before FastMCP
+    initialization to ensure our configuration takes precedence.
+
+    If LOG_FORMAT is not set or is empty, does nothing and lets FastMCP
+    configure logging with its default settings.
+
+    Environment variables:
+        LOG_FORMAT: Python logging format string (optional)
+
+    Examples:
+                   - "%(asctime)s agent %(levelname)s [%(name)s] %(message)s"
+                   - "%(levelname)s: %(message)s"
+                   - "[%(name)s] %(message)s"
+
+    Note:
+        Invalid format strings will cause errors when log records are formatted,
+        not during initialization. This typically results in ValueError, KeyError,
+        or AttributeError being raised when logging occurs.
+
+    """
+    log_format = os.getenv("LOG_FORMAT", "").strip()
+
+    # If LOG_FORMAT is not set or empty, do nothing
+    if not log_format:
+        return
+
+    # Create handler for stderr (same as FastMCP default)
+    handler = logging.StreamHandler(sys.stderr)
+
+    # Create formatter with the specified format string
+    # This will raise an error if the format string is invalid (fail fast)
+    formatter = logging.Formatter(log_format)
+    handler.setFormatter(formatter)
+
+    # Configure root logger
+    # This must be done before FastMCP calls logging.basicConfig()
+    logging.root.addHandler(handler)
+    logging.root.setLevel(logging.INFO)

{codeocean_mcp_server-0.7.0 → codeocean_mcp_server-0.7.2}/src/codeocean_mcp_server/models.py

@@ -1,12 +1,40 @@
-from dataclasses import fields, is_dataclass
+from dataclasses import MISSING, fields, is_dataclass
+from dataclasses import Field as DataclassField
 from typing import Any, List, Type, get_args, get_origin, get_type_hints
 
 from pydantic import BaseModel, Field, create_model
 
 
-def dataclass_to_pydantic(
-    data_class: Type[Any], cache: dict[Type[Any], Type[BaseModel]] = None
-) -> Type[BaseModel]:
+def _get_field_info(field: DataclassField) -> Any:
+    """Get Pydantic field info from dataclass field.
+
+    Args:
+        field: Dataclass field to convert
+
+    Returns:
+        Pydantic field info (Field, Ellipsis, or default value)
+
+    """
+    default = field.default
+    has_description = field.metadata and "description" in field.metadata
+
+    if has_description:
+        description = field.metadata["description"]
+        if default is MISSING:
+            # Required field with description
+            return Field(description=description)
+        else:
+            # Optional field with default and description
+            return Field(default=default, description=description)
+    elif default is MISSING:
+        # Required field without description
+        return ...
+    else:
+        # Optional field with default but no description
+        return default
+
+
+def dataclass_to_pydantic(data_class: Type[Any], cache: dict[Type[Any], Type[BaseModel]] = None) -> Type[BaseModel]:
     """Convert a dataclass to Pydantic model.
 
     Recursively convert a frozen @dataclass (and nested dataclasses)
@@ -17,23 +45,16 @@ def dataclass_to_pydantic(
         cache = {}
     if data_class in cache:
         return cache[data_class]
-    assert is_dataclass(data_class), (
-        f"{data_class.__name__} is not a dataclass"
-    )
+    assert is_dataclass(data_class), f"{data_class.__name__} is not a dataclass"
 
     # 1) Resolve all annotations to real types (no strings)
-    module_ns = vars(
-        __import__(data_class.__module__, fromlist=["*"])
-    )
-    type_hints = get_type_hints(
-        data_class, globalns=module_ns, localns=module_ns
-    )
+    module_ns = vars(__import__(data_class.__module__, fromlist=["*"]))
+    type_hints = get_type_hints(data_class, globalns=module_ns, localns=module_ns)
 
     definitions: dict[str, tuple[type, Any]] = {}
     for field in fields(data_class):
         # Use the evaluated hint if available, else the raw annotation
         typ = type_hints.get(field.name, field.type)
-        default = field.default
         field_type = typ
         origin = get_origin(typ)
         args = get_args(typ)
@@ -48,23 +69,13 @@ def dataclass_to_pydantic(
             nested_model = dataclass_to_pydantic(args[0], cache)
             field_type = List[nested_model]
 
-        # 4) Handle field with description from metadata
-        field_info = default
-        if field.metadata and "description" in field.metadata:
-            # Create a Pydantic Field with description
-            field_info = Field(
-                default=default, description=field.metadata["description"]
-            )
+        # 4) Get Pydantic field info
+        field_info = _get_field_info(field)
 
         definitions[field.name] = (field_type, field_info)
 
     # 5) Dynamically create the Pydantic model
-    model = create_model(
-        f"{data_class.__name__}Model",
-        __base__=BaseModel,
-        __doc__=data_class.__doc__,
-        **definitions
-    )
+    model = create_model(f"{data_class.__name__}Model", __base__=BaseModel, __doc__=data_class.__doc__, **definitions)
 
     # 6) Override the schema generation to include description from docstring
     if data_class.__doc__:

{codeocean_mcp_server-0.7.0 → codeocean_mcp_server-0.7.2}/src/codeocean_mcp_server/server.py

@@ -3,6 +3,7 @@ import os
 from codeocean import CodeOcean
 from mcp.server.fastmcp import FastMCP
 
+from codeocean_mcp_server.logging_config import configure_logging
 from codeocean_mcp_server.tools import (
     capsules,
     computations,
@@ -13,20 +14,18 @@ from codeocean_mcp_server.tools import (
 
 def main():
     """Run the MCP server."""
+    configure_logging()
     domain = os.getenv("CODEOCEAN_DOMAIN")
     token = os.getenv("CODEOCEAN_TOKEN")
     if not domain or not token:
-        raise ValueError(
-            "Environment variables CODEOCEAN_DOMAIN and " "CODEOCEAN_TOKEN must be set."
-        )
+        raise ValueError("Environment variables CODEOCEAN_DOMAIN and CODEOCEAN_TOKEN must be set.")
     agent_id = os.getenv("AGENT_ID", "AI Agent")
     client = CodeOcean(domain=domain, token=token, agent_id=agent_id)
 
     mcp = FastMCP(
         name="Code Ocean",
         instructions=(
-            f"MCP server for Code Ocean: search & run capsules, "
-            f"pipelines, and assets using Code Ocean domain {domain}."
+            f"MCP server for Code Ocean: search & run capsules, pipelines, and assets using Code Ocean domain {domain}."
         ),
     )
 

{codeocean_mcp_server-0.7.0 → codeocean_mcp_server-0.7.2}/src/codeocean_mcp_server/tools/capsules.py

@@ -22,8 +22,7 @@ def add_tools(mcp: FastMCP, client: CodeOcean):
 
     @mcp.tool(
         description=(
-            str(client.capsules.search_capsules.__doc__)
-            + "Use only for capsule searches. "
+            str(client.capsules.search_capsules.__doc__) + "Use only for capsule searches. "
             "Provide only the minimal required parameters (e.g. limit=10); "
             "do not include optional params "
             "like sort_by or sort_order unless requested."
@@ -36,8 +35,7 @@ def add_tools(mcp: FastMCP, client: CodeOcean):
 
     @mcp.tool(
         description=(
-            str(client.capsules.search_pipelines.__doc__)
-            + "Use only for pipeline searches. "
+            str(client.capsules.search_pipelines.__doc__) + "Use only for pipeline searches. "
             "Provide only the minimal required parameters (e.g. limit=10); "
             "do not include optional params "
             "like sort_by or sort_order unless requested."
@@ -60,16 +58,12 @@ def add_tools(mcp: FastMCP, client: CodeOcean):
         attach_params: list[DataAssetAttachParamsModel],
     ) -> list[DataAssetAttachResults]:
         """Attach data assets to a capsule."""
-        params = [
-            DataAssetAttachParams(**p.model_dump(exclude_none=True))
-            for p in attach_params
-        ]
+        params = [DataAssetAttachParams(**p.model_dump(exclude_none=True)) for p in attach_params]
         return client.capsules.attach_data_assets(capsule_id, params)
 
     @mcp.tool(
         description=(
-            str(client.capsules.get_capsule.__doc__)
-            + "Use only to fetch metadata for a known capsule ID. "
+            str(client.capsules.get_capsule.__doc__) + "Use only to fetch metadata for a known capsule ID. "
             "Do not use for searching."
         )
     )

{codeocean_mcp_server-0.7.0 → codeocean_mcp_server-0.7.2}/src/codeocean_mcp_server/tools/computations.py

@@ -23,8 +23,7 @@ def add_tools(mcp: FastMCP, client: CodeOcean):
 
     @mcp.tool(
         description=(
-            str(client.computations.run_capsule.__doc__)
-            + "Typical workflow: 1) run_capsule() to start execution "
+            str(client.computations.run_capsule.__doc__) + "Typical workflow: 1) run_capsule() to start execution "
             "2) wait_until_completed() to monitor progress "
             "3) list_computation_results() and get_result_file_urls() "
             "to retrieve outputs."
@@ -41,28 +40,21 @@ def add_tools(mcp: FastMCP, client: CodeOcean):
         computation = client.computations.get_computation(computation_id)
         return client.computations.wait_until_completed(computation)
 
-
     @mcp.tool(
         description=(
-            str(client.computations.list_computation_results.__doc__)
-            + " computation_id is required as string"
+            str(client.computations.list_computation_results.__doc__) + " computation_id is required as string"
         )
     )
     def list_computation_results(computation_id: str) -> Folder:
         """List the output files generated by a completed computation."""
         return client.computations.list_computation_results(computation_id)
 
-
     @mcp.tool(description=(client.computations.get_result_file_urls.__doc__))
     def get_result_file_urls(computation_id: str, file_path: str) -> FileURLs:
         """Get view and download URLs for a specific result file from computation."""
         return client.computations.get_result_file_urls(computation_id, file_path)
 
-    @mcp.tool(
-        description=(
-            "Use when you want to read the content of a file from a computation"
-        )
-    )
+    @mcp.tool(description=("Use when you want to read the content of a file from a computation"))
     def download_and_read_a_file_from_computation(computation_id: str, file_path: str) -> str:
         """Download a file using the provided URL and return its content."""
         file_urls = client.computations.get_result_file_urls(computation_id, file_path)

{codeocean_mcp_server-0.7.0 → codeocean_mcp_server-0.7.2}/src/codeocean_mcp_server/tools/data_assets.py

@@ -50,11 +50,7 @@ def add_tools(mcp: FastMCP, client: CodeOcean):
         """Get view and download URLs for a specific file in a data asset."""
         return client.data_assets.get_data_asset_file_urls(data_asset_id, file_path)
 
-    @mcp.tool(
-        description=(
-            "Use when you want to read the content of a file from a data asset"
-        )
-    )
+    @mcp.tool(description=("Use when you want to read the content of a file from a data asset"))
     def download_and_read_a_file_from_data_asset(data_asset_id: str, file_path: str) -> str:
         """Download a file using the provided URL and return its content."""
         file_urls = client.data_assets.get_data_asset_file_urls(data_asset_id, file_path)

{codeocean_mcp_server-0.7.0 → codeocean_mcp_server-0.7.2}/tests/bedrock_tools_converter.py

@@ -11,8 +11,6 @@ from mcp.types import Tool
 _NAME_PATTERN = re.compile(r"^[A-Za-z0-9_-]{1,64}$")
 
 
-
-
 def prune_schema(schema: Dict[str, Any]) -> Dict[str, Any]:
     """Recursively prune forbidden keys from a schema."""
     forbidden_keys = {"anyOf", "$schema", "$ref"}
@@ -47,9 +45,7 @@ def validate_schema(schema: Dict[str, Any]) -> None:
     Draft202012Validator.check_schema(schema)
 
 
-def convert_tool_format(
-    tools: List[Tool], model: str
-) -> Dict[str, List[Dict[str, Any]]]:
+def convert_tool_format(tools: List[Tool], model: str) -> Dict[str, List[Dict[str, Any]]]:
     """Convert MCP tools into a Bedrock Draft 2020-12-compliant toolConfig."""
     # For other models, we need to convert tools to the Bedrock format
     converted = []

{codeocean_mcp_server-0.7.0 → codeocean_mcp_server-0.7.2}/tests/test_multi_tool_calling.py

@@ -36,7 +36,7 @@ def check_diff(expected_response: dict, response: dict) -> None:
 
 
 def test_prompt_generates_correct_tool_usage_sequence(
-    agentic_prompt_chain:dict = agentic_prompt_chain,
+    agentic_prompt_chain: dict = agentic_prompt_chain,
 ):
     """Test that the prompt generates the expected sequence of tool calls in the correct order."""
     responses = []

{codeocean_mcp_server-0.7.0 → codeocean_mcp_server-0.7.2}/tests/test_tool_calling.py

@@ -67,9 +67,7 @@ test_response = [
         "prompt": "get capsules - filter capsules where tags = 'brain'",
         "expected": {
             "name": "search_capsules",
-            "input": {
-                "search_params": {"filters": [{"key": "tags", "value": "brain"}]}
-            },
+            "input": {"search_params": {"filters": [{"key": "tags", "value": "brain"}]}},
         },
     },
     # --------------------------------------------------------------
@@ -193,9 +191,7 @@ test_response = [
         "prompt": "get data assets - filter data assets where tags = 'genomics'",
         "expected": {
             "name": "search_data_assets",
-            "input": {
-                "search_params": {"filters": [{"key": "tags", "value": "genomics"}]}
-            },
+            "input": {"search_params": {"filters": [{"key": "tags", "value": "genomics"}]}},
         },
     },
     {
@@ -219,10 +215,7 @@ test_response = [
     },
     {
         "id": "search_data_assets_complex_external_ml",
-        "prompt": (
-            "find 15 external data assets that, "
-            "sorted by size descending, query for 'machine learning'"
-        ),
+        "prompt": ("find 15 external data assets that, sorted by size descending, query for 'machine learning'"),
         "expected": {
             "name": "search_data_assets",
             "input": {
@@ -407,9 +400,7 @@ test_response = [
             "name": "update_metadata",
             "input": {
                 "data_asset_id": "data_asset102",
-                "update_params": {
-                    "custom_metadata": {"key1": "value1", "key2": "value2"}
-                },
+                "update_params": {"custom_metadata": {"key1": "value1", "key2": "value2"}},
             },
         },
     },