@yeyuan98/opencode-bioresearcher-plugin 1.5.0 → 1.5.1

package/dist/skills/env-jsonc-setup/SKILL.md

@@ -1,206 +1,206 @@
----
-name: env-jsonc-setup
-description: Setup env.jsonc configuration file for db-tools module - guides user through creating database connection config with interactive questions
-allowedTools:
-  - Question
-  - Write
-  - Read
----
-
-# Database Configuration Setup
-
-This skill guides users through creating an `env.jsonc` file for configuring db-tools module.
-
-## Overview
-
-The `env.jsonc` file contains database connection settings for db-tools. This skill:
-1. Collects database preferences (type, host, port, credentials)
-2. Generates a properly formatted `env.jsonc` file with comments
-3. Places it in the current working directory
-
-## Workflow
-
-Follow these steps EXACTLY as described.
-
-### Step 1: Determine Database Type
-
-Use the question tool to ask the user which database type they want to configure:
-
-Options:
-- **MySQL** (Recommended for local development, SQL databases)
-- **MongoDB** (For NoSQL databases, MongoDB Atlas)
-
-### Step 2: Ask Connection Details
-
-Based on the database type selected, use the question tool to gather connection details.
-
-#### For MySQL:
-Ask for:
-1. **Host** (default: "localhost")
-2. **Port** (default: 3306)
-3. **Database name** (required)
-4. **Username** (required)
-5. **Password** (optional, can be empty)
-6. **Connection timeout** (default: 10000 ms)
-
-#### For MongoDB:
-Ask for:
-1. **Connection method**:
-   - Individual parameters (host, port, username, password)
-   - Connection URI (recommended for Atlas)
-
-If "Individual parameters":
-   - **Host** (default: "localhost")
-   - **Port** (default: 27017)
-   - **Database name** (required)
-   - **Username** (optional)
-   - **Password** (optional)
-   - **Connection timeout** (default: 10000 ms)
-
-If "Connection URI":
-   - **MongoDB URI** (required, e.g., `mongodb+srv://user:pass@cluster.mongodb.net/db`)
-   - **Database name** (required)
-   - **Connection timeout** (default: 10000 ms)
-
-### Step 3: Check if env.jsonc Already Exists
-
-Check if `env.jsonc` exists in the working directory:
-
-```bash
-test -f "env.jsonc" && echo "exists" || echo "not exists"
-```
-
-If the file exists:
-- Use the question tool to ask: "env.jsonc already exists. Overwrite?"
-  - Options: "Yes, overwrite", "No, keep existing"
-
-If user selects "No", skip to Step 5 and report that no changes were made.
-
-If user selects "Yes" or file doesn't exist, continue to Step 4.
-
-### Step 4: Generate and Write env.jsonc
-
-Create the `env.jsonc` file based on user's answers using the Write tool.
-
-#### Template for MySQL:
-
-```jsonc
-{
-  "db-tools": {
-    "type": "mysql",
-    "host": "<HOST>",
-    "port": <PORT>,
-    "database": "<DATABASE>",
-    "username": "<USERNAME>",
-    "password": "<PASSWORD>",
-    "connectionTimeout": <TIMEOUT>
-  }
-}
-```
-
-Replace placeholders with user-provided values. If `password` is empty, use `""`.
-
-#### Template for MongoDB (Individual Parameters):
-
-```jsonc
-{
-  "db-tools": {
-    "type": "mongodb",
-    "host": "<HOST>",
-    "port": <PORT>,
-    "database": "<DATABASE>",
-    "username": "<USERNAME>",
-    "password": "<PASSWORD>",
-    "connectionTimeout": <TIMEOUT>
-  }
-}
-```
-
-Replace placeholders with user-provided values. If `username` or `password` is empty, use `""`.
-
-#### Template for MongoDB (Connection URI):
-
-```jsonc
-{
-  "db-tools": {
-    "type": "mongodb",
-    "uri": "<MONGODB_URI>",
-    "database": "<DATABASE>",
-    "connectionTimeout": <TIMEOUT>
-  }
-}
-```
-
-Replace placeholders with user-provided values.
-
-Use the Write tool to create `env.jsonc` with the generated content in the working directory.
-
-### Step 5: Provide Usage Instructions
-
-After the file is created, provide the user with:
-
-1. **Configuration location**: `env.jsonc` in current working directory
-2. **Database type**: The type configured
-3. **Quick test command** (optional suggestion):
-
-For testing connection:
-- "Try using dbListTables tool to verify the connection works"
-- "The configuration will be automatically loaded on first db-tools usage"
-
-## Important Notes
-
-- The `env.jsonc` file uses JSONC format (JSON with comments)
-- Sensitive information like passwords are stored in plain text
-- Add `env.jsonc` to `.gitignore` to avoid committing credentials
-- The configuration is automatically loaded by db-tools on first tool use
-- Comments in the file help document different use cases
-
-## Error Handling
-
-If at any point the user provides invalid input:
-- Ask again with the same question
-- Provide helpful hints (e.g., "Port must be a number between 1-65535")
-
-## Examples
-
-### MySQL Local Development:
-```jsonc
-{
-  "db-tools": {
-    "type": "mysql",
-    "host": "localhost",
-    "port": 3306,
-    "database": "devdb",
-    "username": "root",
-    "password": "",
-    "connectionTimeout": 10000
-  }
-}
-```
-
-### MongoDB Local:
-```jsonc
-{
-  "db-tools": {
-    "type": "mongodb",
-    "host": "localhost",
-    "port": 27017,
-    "database": "mydb",
-    "username": "admin",
-    "password": "secret",
-    "connectionTimeout": 10000
-  }
-}
-```
-
-### MongoDB Atlas:
-```jsonc
-{
-  "db-tools": {
-    "type": "mongodb",
-    "uri": "mongodb+srv://user:pass@cluster0.mongodb.net/proddb?authSource=admin",
-    "database": "proddb",
-    "connectionTimeout": 10000
-  }
-}
-```
+---
+name: env-jsonc-setup
+description: Setup env.jsonc configuration file for db-tools module - guides user through creating database connection config with interactive questions
+allowedTools:
+  - Question
+  - Write
+  - Read
+---
+
+# Database Configuration Setup
+
+This skill guides users through creating an `env.jsonc` file for configuring db-tools module.
+
+## Overview
+
+The `env.jsonc` file contains database connection settings for db-tools. This skill:
+1. Collects database preferences (type, host, port, credentials)
+2. Generates a properly formatted `env.jsonc` file with comments
+3. Places it in the current working directory
+
+## Workflow
+
+Follow these steps EXACTLY as described.
+
+### Step 1: Determine Database Type
+
+Use the question tool to ask the user which database type they want to configure:
+
+Options:
+- **MySQL** (Recommended for local development, SQL databases)
+- **MongoDB** (For NoSQL databases, MongoDB Atlas)
+
+### Step 2: Ask Connection Details
+
+Based on the database type selected, use the question tool to gather connection details.
+
+#### For MySQL:
+Ask for:
+1. **Host** (default: "localhost")
+2. **Port** (default: 3306)
+3. **Database name** (required)
+4. **Username** (required)
+5. **Password** (optional, can be empty)
+6. **Connection timeout** (default: 10000 ms)
+
+#### For MongoDB:
+Ask for:
+1. **Connection method**:
+   - Individual parameters (host, port, username, password)
+   - Connection URI (recommended for Atlas)
+
+If "Individual parameters":
+   - **Host** (default: "localhost")
+   - **Port** (default: 27017)
+   - **Database name** (required)
+   - **Username** (optional)
+   - **Password** (optional)
+   - **Connection timeout** (default: 10000 ms)
+
+If "Connection URI":
+   - **MongoDB URI** (required, e.g., `mongodb+srv://user:pass@cluster.mongodb.net/db`)
+   - **Database name** (required)
+   - **Connection timeout** (default: 10000 ms)
+
+### Step 3: Check if env.jsonc Already Exists
+
+Check if `env.jsonc` exists in the working directory:
+
+```bash
+test -f "env.jsonc" && echo "exists" || echo "not exists"
+```
+
+If the file exists:
+- Use the question tool to ask: "env.jsonc already exists. Overwrite?"
+  - Options: "Yes, overwrite", "No, keep existing"
+
+If user selects "No", skip to Step 5 and report that no changes were made.
+
+If user selects "Yes" or file doesn't exist, continue to Step 4.
+
+### Step 4: Generate and Write env.jsonc
+
+Create the `env.jsonc` file based on user's answers using the Write tool.
+
+#### Template for MySQL:
+
+```jsonc
+{
+  "db-tools": {
+    "type": "mysql",
+    "host": "<HOST>",
+    "port": <PORT>,
+    "database": "<DATABASE>",
+    "username": "<USERNAME>",
+    "password": "<PASSWORD>",
+    "connectionTimeout": <TIMEOUT>
+  }
+}
+```
+
+Replace placeholders with user-provided values. If `password` is empty, use `""`.
+
+#### Template for MongoDB (Individual Parameters):
+
+```jsonc
+{
+  "db-tools": {
+    "type": "mongodb",
+    "host": "<HOST>",
+    "port": <PORT>,
+    "database": "<DATABASE>",
+    "username": "<USERNAME>",
+    "password": "<PASSWORD>",
+    "connectionTimeout": <TIMEOUT>
+  }
+}
+```
+
+Replace placeholders with user-provided values. If `username` or `password` is empty, use `""`.
+
+#### Template for MongoDB (Connection URI):
+
+```jsonc
+{
+  "db-tools": {
+    "type": "mongodb",
+    "uri": "<MONGODB_URI>",
+    "database": "<DATABASE>",
+    "connectionTimeout": <TIMEOUT>
+  }
+}
+```
+
+Replace placeholders with user-provided values.
+
+Use the Write tool to create `env.jsonc` with the generated content in the working directory.
+
+### Step 5: Provide Usage Instructions
+
+After the file is created, provide the user with:
+
+1. **Configuration location**: `env.jsonc` in current working directory
+2. **Database type**: The type configured
+3. **Quick test command** (optional suggestion):
+
+For testing connection:
+- "Try using dbListTables tool to verify the connection works"
+- "The configuration will be automatically loaded on first db-tools usage"
+
+## Important Notes
+
+- The `env.jsonc` file uses JSONC format (JSON with comments)
+- Sensitive information like passwords are stored in plain text
+- Add `env.jsonc` to `.gitignore` to avoid committing credentials
+- The configuration is automatically loaded by db-tools on first tool use
+- Comments in the file help document different use cases
+
+## Error Handling
+
+If at any point the user provides invalid input:
+- Ask again with the same question
+- Provide helpful hints (e.g., "Port must be a number between 1-65535")
+
+## Examples
+
+### MySQL Local Development:
+```jsonc
+{
+  "db-tools": {
+    "type": "mysql",
+    "host": "localhost",
+    "port": 3306,
+    "database": "devdb",
+    "username": "root",
+    "password": "",
+    "connectionTimeout": 10000
+  }
+}
+```
+
+### MongoDB Local:
+```jsonc
+{
+  "db-tools": {
+    "type": "mongodb",
+    "host": "localhost",
+    "port": 27017,
+    "database": "mydb",
+    "username": "admin",
+    "password": "secret",
+    "connectionTimeout": 10000
+  }
+}
+```
+
+### MongoDB Atlas:
+```jsonc
+{
+  "db-tools": {
+    "type": "mongodb",
+    "uri": "mongodb+srv://user:pass@cluster0.mongodb.net/proddb?authSource=admin",
+    "database": "proddb",
+    "connectionTimeout": 10000
+  }
+}
+```