Merge branch 'release/6.3.0'

Author: dermatologist

CHANGELOG.md

@@ -2,14 +2,16 @@
 
 ## [Unreleased](https://github.com/dermatologist/pyomop/tree/HEAD)
 
-[Full Changelog](https://github.com/dermatologist/pyomop/compare/v6.1.0...HEAD)
+[Full Changelog](https://github.com/dermatologist/pyomop/compare/v6.2.3...HEAD)
 
 **Implemented enhancements:**
 
+- Update MCP server [\#255](https://github.com/dermatologist/pyomop/issues/255)
 - Add PyHealth compatible export function [\#243](https://github.com/dermatologist/pyomop/pull/243) ([Copilot](https://github.com/apps/copilot-swe-agent))
 
 **Merged pull requests:**
 
+- Add missing MCP tools and HTTP transport support [\#256](https://github.com/dermatologist/pyomop/pull/256) ([Copilot](https://github.com/apps/copilot-swe-agent))
 - Feature/fix thread 1 [\#254](https://github.com/dermatologist/pyomop/pull/254) ([dermatologist](https://github.com/dermatologist))
 - Fix LLM query engine bugs and switch to native llama-index embeddings [\#253](https://github.com/dermatologist/pyomop/pull/253) ([Copilot](https://github.com/apps/copilot-swe-agent))
 - \[GitHub Dependents Info\] Updated markdown file [\#252](https://github.com/dermatologist/pyomop/pull/252) ([github-actions[bot]](https://github.com/apps/github-actions))
@@ -47,7 +49,10 @@
 - build\(deps\): bump urllib3 from 1.26.18 to 1.26.19 [\#167](https://github.com/dermatologist/pyomop/pull/167) ([dependabot[bot]](https://github.com/apps/dependabot))
 - build\(deps\): bump jinja2 from 3.0.1 to 3.1.3 [\#161](https://github.com/dermatologist/pyomop/pull/161) ([dependabot[bot]](https://github.com/apps/dependabot))
 - Feature/llm llama index 1 [\#159](https://github.com/dermatologist/pyomop/pull/159) ([dermatologist](https://github.com/dermatologist))
-- build\(deps\): bump actions/setup-python from 2.3.1 to 5.0.0 [\#155](https://github.com/dermatologist/pyomop/pull/155) ([dependabot[bot]](https://github.com/apps/dependabot))
+
+## [v6.2.3](https://github.com/dermatologist/pyomop/tree/v6.2.3) (2025-12-24)
+
+[Full Changelog](https://github.com/dermatologist/pyomop/compare/v6.1.0...v6.2.3)
 
 ## [v6.1.0](https://github.com/dermatologist/pyomop/tree/v6.1.0) (2025-09-29)
 

README.md

@@ -202,19 +202,9 @@ pyomop includes an MCP (Model Context Protocol) server that exposes tools for in
   <img src="https://github.com/dermatologist/pyomop/blob/develop/notes/pyomop-mcp.gif" />
 </p>
 
-### Starting the MCP Server
-
-To start the MCP server for stdio interaction:
-
-```bash
-# Using the main CLI
-pyomop --mcp-server
-
-```
-
 #### Usage with MCP Clients
 
-The server communicates via stdio and can be used with any MCP-compatible client. Example configuration for [vscode](/.vscode/mcp.json):
+The MCP server can be used with any MCP-compatible client such as Claude desktop. Example configuration for [VSCODE](/.vscode/mcp.json) as below is already provided in the repository. So if you are viewing this in VSCODE, you can start server and enable tools directly in Copilot.
 
 ```json
 {
@@ -237,8 +227,38 @@ The server communicates via stdio and can be used with any MCP-compatible client
 - **get_single_table_info**: Get detailed table information, including foreign keys
 - **get_usable_table_names**: Get a list of all available table names
 - **run_sql**: Execute SQL statements with error handling
+- **example_query**: Get example queries for specific OMOP CDM tables from OHDSI QueryLibrary
+- **check_sql**: Validate SQL query syntax before execution
 
 * create_cdm and create_eunomia support only local sqlite databases to avoid inadvertent data loss in production databases.
+
+#### HTTP Transport Support
+
+The MCP server now supports both stdio (default) and HTTP transports:
+
+**Stdio transport (default):**
+```bash
+pyomop --mcp-server
+# or
+pyomop-mcp-server
+```
+
+**HTTP transport:**
+```bash
+pyomop-mcp-server-http
+# or with custom host/port
+pyomop-mcp-server-http --host 0.0.0.0 --port 8000
+# or via Python module
+python -m pyomop.mcp.server --http --host 0.0.0.0 --port 8000
+```
+
+To use HTTP transport, install additional dependencies:
+```bash
+pip install pyomop[http]
+# or for both LLM and HTTP features
+pip install pyomop[llm,http]
+```
+
 #### Available Prompts
 
 - **query_execution_steps**: Provides step-by-step guidance for executing database queries based on free text instructions

pyproject.toml

@@ -74,6 +74,7 @@ source-exclude = ["tests/*", "examples/*", "docs/*", "notes/*", "notebooks/*"]
 [project.scripts]
 pyomop = "pyomop.main:main_routine"
 pyomop-mcp-server = "pyomop.mcp.server:main_cli"
+pyomop-mcp-server-http = "pyomop.mcp.server:main_http_cli"
 
 [project.optional-dependencies]
 llm = [
@@ -85,6 +86,10 @@ llm = [
     "langchain-openai",
     "dhti-elixir-base",
 ]
+http = [
+    "starlette",
+    "uvicorn",
+]
 
 [tool.hatch.build.targets.wheel]
 packages = ["src/pyomop"]

src/pyomop/engine_factory.py

@@ -192,6 +192,16 @@ def async_session(self):
             return async_session
         return None
 
+    async def dispose(self) -> None:
+        """Dispose of the engine and close all connections.
+
+        This should be called when done with database operations to
+        ensure proper cleanup and avoid hanging.
+        """
+        if self._engine is not None:
+            await self._engine.dispose()
+            self._engine = None
+
     @db.setter
     def db(self, value):
         self._db = value

src/pyomop/main.py

@@ -5,7 +5,9 @@
 """
 
 import asyncio
+
 import click
+
 from . import __version__
 from .engine_factory import CdmEngineFactory
 from .vocabulary import CdmVocabulary
@@ -105,23 +107,29 @@ def cli(
     if create:
         click.echo(f"Creating CDM {version} tables in {dbtype} database {name}")
         cdm = CdmEngineFactory(dbtype, host, port, user, pw, name, schema)
-        # initialize default engine
-        engine = cdm.engine
-        if version == "cdm54":
-            from .cdm54 import Base
+        try:
+            # initialize default engine
+            engine = cdm.engine
+            if version == "cdm54":
+                from .cdm54 import Base
 
-            asyncio.run(cdm.init_models(Base.metadata))
-        else:  # default cdm6
-            from .cdm6 import Base
+                asyncio.run(cdm.init_models(Base.metadata))
+            else:  # default cdm6
+                from .cdm6 import Base
 
-            asyncio.run(cdm.init_models(Base.metadata))
-        click.echo("Done")
+                asyncio.run(cdm.init_models(Base.metadata))
+            click.echo("Done")
+        finally:
+            asyncio.run(cdm.dispose())
     if vocab != "":
         click.echo(f"Creating CDM {version} vocabulary in {dbtype} database {name}")
         cdm = CdmEngineFactory(dbtype, host, port, user, pw, name, schema)
-        _vocab = CdmVocabulary(cdm)
-        asyncio.run(_vocab.create_vocab(vocab))
-        click.echo("Done")
+        try:
+            _vocab = CdmVocabulary(cdm)
+            asyncio.run(_vocab.create_vocab(vocab))
+            click.echo("Done")
+        finally:
+            asyncio.run(cdm.dispose())
 
     if input_path:
         click.echo(f"Loading FHIR data from {input_path} into {dbtype} database {name}")
@@ -165,13 +173,16 @@ def cli(
                 click.echo(f"Data written to temporary file: {temp_file.name}")
         # Load CSV into OMOP tables using mapping
         loader = CdmCsvLoader(cdm)
-        asyncio.run(
-            loader.load(
-                csv_path=temp_file.name,
-                chunk_size=500,
+        try:
+            asyncio.run(
+                loader.load(
+                    csv_path=temp_file.name,
+                    chunk_size=500,
+                )
             )
-        )
-        click.echo("Done")
+            click.echo("Done")
+        finally:
+            asyncio.run(cdm.dispose())
 
     if eunomia_dataset:
         click.echo(
@@ -199,7 +210,7 @@ def cli(
                     dataset_name=eunomia_dataset,
                     cdm_version=version,
                     input_format="csv",
-                    verbose=True
+                    verbose=True,
                 )
             )
             click.echo(f"Loaded dataset into configured database: {name}")
@@ -214,19 +225,26 @@ def cli(
         except Exception as e:
             click.echo(f"Error creating/populating cohort table: {e}", err=True)
             raise
+        finally:
+            asyncio.run(cdm.dispose())
         click.echo("Done")
     if cdm and connection_info:
         click.echo(click.style("Database connection information:", fg="green"))
         click.echo(cdm.print_connection_info())
 
     if mcp_server:
         import sys
+
         click.echo("Starting pyomop MCP server...")
         try:
             from .mcp import mcp_server_main
+
             asyncio.run(mcp_server_main())
         except ImportError:
-            click.echo("MCP server requires 'mcp' package. Install with: pip install mcp", err=True)
+            click.echo(
+                "MCP server requires 'mcp' package. Install with: pip install mcp",
+                err=True,
+            )
             sys.exit(1)
         except KeyboardInterrupt:
             click.echo("MCP server stopped.")
@@ -236,8 +254,12 @@ def cli(
 
     if pyhealth_path:
         import sys
-        click.echo(f"Exporting PyHealth tables to {pyhealth_path} from {dbtype} database {name}")
+
+        click.echo(
+            f"Exporting PyHealth tables to {pyhealth_path} from {dbtype} database {name}"
+        )
         from .pyhealth import PyHealthExport
+
         cdm = CdmEngineFactory(dbtype, host, port, user, pw, name, schema)
         exporter = PyHealthExport(cdm, export_path=pyhealth_path)
         try:
@@ -246,6 +268,9 @@ def cli(
         except Exception as e:
             click.echo(f"Error exporting PyHealth tables: {e}", err=True)
             sys.exit(1)
+        finally:
+            asyncio.run(cdm.dispose())
+
 
 def main_routine():
     """Top-level runner used by ``python -m pyomop``."""