Repository: fastomop/omcp
Pull request #2: [Fix] Hotfix
Author: login: sshenzha
Created: 2025-04-22T19:10:09Z | Merged: 2025-04-22T21:38:58Z

Added a new section to clarify Git LFS to pull Synthea, and changed the Claude Desktop config file


Diff:
diff --git a/docs/index.md b/docs/index.md
index 82c0e75..4dbf9bb 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -38,7 +38,7 @@ OMCP (OMOP Model Context Protocol) is an open-source server that enables Large L
 
 ### Getting Started
 
-See our [Installation Guide](./installation.md) to set up OMCP in your environment. The [API Documentation](./api/index.md) provides details on available endpoints and interaction patterns.
+See our [Installation Guide](./installation.md) to set up OMCP in your environment.
 
 ### Architecture
 
@@ -62,4 +62,4 @@ OMCP sits between LLMs and OMOP CDM databases, providing a structured, secure in
 
 ### License
 
-OMCP is available under the [MIT License](./license.md).
+OMCP is available under the [MIT License](https://opensource.org/license/mit).
diff --git a/docs/installation.md b/docs/installation.md
index 4445944..46b0a77 100644
--- a/docs/installation.md
+++ b/docs/installation.md
@@ -16,6 +16,7 @@ We appreciate your patience and feedback as we work toward a stable release!
 ### Prerequisites
 
 - [Git](https://git-scm.com/)
+- [Git LFS](https://git-lfs.com/)
 - [uv (Python package installer) ](https://docs.astral.sh/uv/)
     - On MacOS/Linux
     ```bash
@@ -28,7 +29,6 @@ We appreciate your patience and feedback as we work toward a stable release!
 
 - Python 3.13 or higher (Let UV install and manage python versions within a virtual environment)
 
-
 ### Step 1: Clone the Repository
 
 ```bash
@@ -48,7 +48,7 @@ uv sync --extra duckdb
 
 #### With PostgreSQL Support
 
-!!!warning
+!!! warning
     Not implemented yet.
 
 ```bash
@@ -61,11 +61,29 @@ uv sync --extra postgres
 source .venv/bin/activate  # On Windows use: .venv\Scripts\activate
 ```
 
-
 ## Using the Synthetic Database 🗄️
 
 OMCP comes with a synthetic OMOP database (located at `/synthetic_data/synthea.duckdb`) for testing and development purposes. This database follows the OMOP Common Data Model and contains fictional patient data available at [Synthea](https://synthetichealth.github.io/synthea/).
 
+### Retrieving Synthea.duckdb
+Since the database is a rather large file, the actual database has been replaced by a Git LFS pointer, you should see something like this inside `synthea.duckdb`:
+```
+version https://git-lfs.github.com/spec/v1
+oid sha256:d753b619a8650c966ce219daa35b4126fb9307b790e49f0244646cb3b796feab
+size 21508096
+```
+
+to retrieve the database:
+
+```bash
+git lfs install
+```
+and then:
+
+```bash
+git lfs pull
+```
+
 ### Setting Up the Environment Variable
 
 Create a `.env` file in your project root with the connection string:
@@ -114,7 +132,6 @@ OMCP provides a Model Context Protocol server that can integrate with Claude Des
 Download and install [Claude Desktop](https://claude.ai/download) from the official website.
 On Linux, use https://github.com/aaddrick/claude-desktop-debian/ or similar until an official release becomes available.
 
-
 ### Step 2: Configure Claude Desktop to Use OMCP
 
 1. Open or create the Claude Desktop configuration file:
@@ -123,11 +140,15 @@ On Linux, use https://github.com/aaddrick/claude-desktop-debian/ or similar unti
 # Linux
 mkdir -p ~/.config/Claude
 nano ~/.config/Claude/claude_desktop_config.json
+```
 
+```bash
 # macOS
 mkdir -p ~/Library/Application\ Support/Claude
 nano ~/Library/Application\ Support/Claude/claude_desktop_config.json
+```
 
+```cmd
 # Windows
 notepad %APPDATA%\Claude\claude_desktop_config.json
 ```
@@ -136,19 +157,21 @@ notepad %APPDATA%\Claude\claude_desktop_config.json
 
 ```json
 {
-    "mcpServers": {
-        "omop_mcp": {
-            "command": "mcp",
-            "args": [
-                "run",
-                "/path/to/omcp/src/omcp/main.py"
-            ]
-        }
+  "mcpServers": {
+    "omop_mcp": {
+      "command": "uv",
+      "args": [
+        "--directory",
+        "/ABSOLUTE/PATH/TO/PARENT/FOLDER THAT CONTAINS main.py",
+        "run",
+        "main.py"
+      ]
     }
+  }
 }
 ```
 
-Replace `/path/to/omcp` with the actual path to your OMCP installation.
+Replace `/ABSOLUTE/PATH/TO/PARENT/FOLDER THAT CONTAINS main.py` with the actual path to your OMCP installation.
 
 ### Step 3: Launch Claude Desktop
 


Reviews:
user: login: vvcb
body: Thank you @shen1802 . Worth rendering these locally to make sure the changes render correctly. Running `mkdocs serve` from the root dir on your branch should spin up a local server.
state: COMMENTED
author_association: CONTRIBUTOR
submitted_at: 2025-04-22T19:42:17Z
user: login: vvcb
body: @shen1802 , thank you for updating the docs.  I have added some comments. Some of the indentation changes break the rendering at least on my setup. Worth comparing how things are currently displayed at https://fastomop.github.io/omcp/installation/ (especially for the warning boxes but also for code blocks)
state: CHANGES_REQUESTED
author_association: CONTRIBUTOR
submitted_at: 2025-04-22T20:20:33Z
user: login: vvcb
state: APPROVED
author_association: CONTRIBUTOR
submitted_at: 2025-04-22T21:36:23Z

Review comments:
diff_hunk: @@ -102,8 +124,8 @@ duckdb -ui synthea.duckdb
 ```
 
 !!! warning
-    DuckDB does not allow multiple processes to open a connection to the database at the same time when at least one of them has write access.
-    To avoid running into problems, close any open connections to the database before running the MCP server.
+DuckDB does not allow multiple processes to open a connection to the database at the same time when at least one of them has write access.
+To avoid running into problems, close any open connections to the database before running the MCP server.
path: docs/installation.md
user: login: vvcb
body: Removing these indentations will move this text outside the warning box. 
created_at: 2025-04-22T20:05:26Z
author_association: CONTRIBUTOR
diff_hunk: @@ -16,18 +16,22 @@ We appreciate your patience and feedback as we work toward a stable release!
 ### Prerequisites
 
 - [Git](https://git-scm.com/)
+- [Git LFS](https://git-lfs.com/)
 - [uv (Python package installer) ](https://docs.astral.sh/uv/)
-    - On MacOS/Linux
-    ```bash
-    curl -LsSf https://astral.sh/uv/install.sh | sh
-    ```
-    - On Windows
-    ```powershell
-    powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"
-    ```
 
-- Python 3.13 or higher (Let UV install and manage python versions within a virtual environment)
+  - On MacOS/Linux
path: docs/installation.md
user: login: vvcb
body: The indentation of the code blocks ensures that these align with the list item that they belong to.
created_at: 2025-04-22T20:06:53Z
author_association: CONTRIBUTOR
diff_hunk: @@ -49,7 +53,7 @@ uv sync --extra duckdb
 #### With PostgreSQL Support
 
 !!!warning
-    Not implemented yet.
+Not implemented yet.
path: docs/installation.md
user: login: vvcb
body: This needs to stay indented to keep the text within the warning box as it is now. 
created_at: 2025-04-22T20:07:53Z
author_association: CONTRIBUTOR
diff_hunk: @@ -136,19 +157,21 @@ notepad %APPDATA%\Claude\claude_desktop_config.json
 
 ```json
 {
-    "mcpServers": {
-        "omop_mcp": {
-            "command": "mcp",
-            "args": [
-                "run",
-                "/path/to/omcp/src/omcp/main.py"
-            ]
-        }
+  "mcpServers": {
path: docs/installation.md
user: login: vvcb
body: This works beautifully and seems to have solved the issue I was having around activating python venv every time I started claude desktop. Thank you.,
created_at: 2025-04-22T20:16:33Z
author_association: CONTRIBUTOR
diff_hunk: @@ -136,19 +157,21 @@ notepad %APPDATA%\Claude\claude_desktop_config.json
 
 ```json
 {
-    "mcpServers": {
-        "omop_mcp": {
-            "command": "mcp",
-            "args": [
-                "run",
-                "/path/to/omcp/src/omcp/main.py"
-            ]
-        }
+  "mcpServers": {
path: docs/installation.md
user: login: vvcb
body: Worth exploring `sse` instead of `stdio` for transport spec as well. 
created_at: 2025-04-22T20:17:42Z
author_association: CONTRIBUTOR

PR comments:
user: login: sshenzha
created_at: 2025-04-22T19:49:45Z
body: @vvcb, I have executed the `mkdocs server` locally and it is looking good :)
author_association: COLLABORATOR
user: login: sshenzha
created_at: 2025-04-22T20:48:15Z
body: @vvcb, apologies for the indentation issue. It should be fixed and fine now. Let me know if it is working for you! 😄  
author_association: COLLABORATOR