@yeyuan98/opencode-bioresearcher-plugin 1.3.1 → 1.4.1

package/dist/skills/pubmed-weekly/SKILL.md

@@ -1,329 +1,329 @@
----
-name: pubmed-weekly
-description: Download PubMed daily update xml.gz files from the past week from NCBI FTP server
-allowedTools:
-  - Bash
-  - Read
-  - Write
-  - Question
-  - parse_pubmed_articleSet
----
-
-# PubMed Weekly Daily Updates Download
-
-This skill downloads PubMed daily update xml.gz files from the past week (Monday-Sunday).
-
-## Workflow Overview
-
-1. **Python Environment Setup** (automatic): Checks for uv, installs via `python-setup-uv` skill if needed
-2. **Date Calculation**: Calculates the past week's date range (Monday-Sunday)
-3. **FTP Listing**: Fetches available xml.gz files from NCBI FTP server
-4. **Filtering**: Filters files to include only those from the past week
-5. **Download**: Downloads filtered files with retry logic (max 3 attempts per file)
-
-## Prerequisites
-- Internet connection
-- Access to NCBI FTP server
-- uv package manager (will be automatically installed if not present)
-
-## Integration with python-setup-uv
-
-This skill integrates with the `python-setup-uv` skill to ensure Python environment is properly configured.
-
-### Prerequisite Check
-
-Before starting the download process:
-
-1. **Check if uv is installed:**
-    ```bash
-    if [ -f "uv" ] || [ -f "uv.exe" ]; then
-      echo "uv already installed"
-    else
-      echo "uv not found, setting up..."
-    fi
-    ```
-
-2. **If uv is not installed:**
-   - Load the `python-setup-uv` skill using the skill tool
-   - Follow all steps EXACTLY as specified in the python-setup-uv skill
-   - Wait for uv installation to complete
-   - Continue with this skill's Step 1 below
-
-3. **After uv is installed:**
-   - The bundled script `pubmed_weekly.py` will be executed using uv
-   - Extract the full script path from the `<skill_files>` section in skill tool output
-
-## Steps
-
-Follow these steps EXACTLY as described.
-
-### Step 1: Calculate Week Date Range
-
-First, determine the date range for the past week (Monday through Sunday).
-
-Extract the full path to `pubmed_weekly.py` from the `<skill_files>` section in the skill tool output.
-
-**For Unix-like shells (Git Bash / macOS / Linux):**
-```bash
-uv run python <skill_path>/pubmed_weekly.py calculate_week
-```
-
-### Step 1: Calculate Week Date Range
-
-First, determine the date range for the past week (Monday through Sunday).
-
-Extract the full path to `pubmed_weekly.py` from the `<skill_files>` section in the skill tool output.
-
-### Step 1: Calculate Week Date Range
-
-First, determine the date range for the past week (Monday through Sunday).
-
-**For Unix-like shells (Git Bash / macOS / Linux):**
-```bash
-uv run python <skill_path>/pubmed_weekly.py calculate_week
-```
-
-**For Windows cmd.exe:**
-```bash
-uv.exe run python <skill_path>\pubmed_weekly.py calculate_week
-```
-
-Replace `<skill_path>` with the full directory path extracted from `<skill_files>`.
-
-This will output the week folder name in format `YYYYMMDD-YYYYMMDD`.
-
-**Expected output format:**
-```
-20250217-20250223
-```
-
-### Step 2: Create Download Directory
-
-The `download_file` command will automatically create the directory structure when needed. No manual directory creation is required.
-
-### Step 3: Fetch FTP File List
-
-Extract the full path to `pubmed_weekly.py` from the `<skill_files>` section and fetch the list of files from the NCBI FTP server.
-
-**For Unix-like shells:**
-```bash
-uv run python <skill_path>/pubmed_weekly.py fetch_files
-```
-
-**For Windows cmd.exe:**
-```bash
-uv.exe run python <skill_path>\pubmed_weekly.py fetch_files
-```
-
-Replace `<skill_path>` with the full directory path extracted from `<skill_files>`.
-
-This will list all daily update xml.gz files available on the FTP server.
-
-**Expected output:**
-```
-pubmed24n1234.xml.gz pubmed24n1235.xml.gz pubmed24n1236.xml.gz
-```
-
-### Step 4: Filter Files for Past Week
-
-Extract the full path to `pubmed_weekly.py` from the `<skill_files>` section and filter the file list for the past week's daily updates.
-
-**For Unix-like shells:**
-```bash
-uv run python <skill_path>/pubmed_weekly.py filter_files "<WEEK>" "<FILE_LIST>"
-```
-
-**For Windows cmd.exe:**
-```bash
-uv.exe run python <skill_path>\pubmed_weekly.py filter_files "<WEEK>" "<FILE_LIST>"
-```
-
-Where:
-- `<skill_path>` is the full directory path extracted from `<skill_files>`
-- `<WEEK>` is the week folder name (e.g., `20250217-20250223`)
-- `<FILE_LIST>` is the output from Step 3 (space-separated filenames, use quotes)
-
-This will return a space-separated list of xml.gz files from the past week.
-
-**Expected output:**
-```
-pubmed24n1234.xml.gz pubmed24n1235.xml.gz pubmed24n1236.xml.gz
-```
-
-### Step 5: Download Files with Retry
-
-Extract the full path to `pubmed_weekly.py` from the `<skill_files>` section and for each file in the filtered list, download to the target directory with retry logic.
-
-**For Unix-like shells:**
-```bash
-for file in <FILE_LIST>; do
-  uv run python <skill_path>/pubmed_weekly.py download_file <WEEK> $file
-done
-```
-
-**For Windows cmd.exe:**
-```bash
-for %f in (<FILE_LIST>) do uv.exe run python <skill_path>\pubmed_weekly.py download_file <WEEK> %f
-```
-
-Where:
-- `<skill_path>` is the full directory path extracted from `<skill_files>`
-- `<FILE_LIST>` is the space-separated list from Step 4
-- `<WEEK>` is the week folder name
-
-Replace `<FILE_LIST>` with the space-separated list from Step 4.
-
-**Download behavior:**
-- Downloads one file at a time
-- Retries up to 3 times if download fails
-- Waits 2 seconds between retry attempts
-- After 3 failed attempts, asks user whether to abort
-
-**If a download fails after 3 retries:**
-Use the question tool to ask:
-- "Abort remaining downloads?" (options: "Yes" / "No")
-
-If user selects "Yes", stop the process and report summary.
-If user selects "No", skip the failed file and continue with the next one.
-
-### Step 6: Verify Downloads
-
-After all downloads complete (or are aborted), verify the downloaded files:
-
-```bash
-ls -lh .download/pubmed-daily/<WEEK>/
-```
-
-Count the number of files downloaded and report the summary to the user.
-
-### Step 7: Parse XML Files to Individual Excel Sheets
-
-For each downloaded `.xml.gz` file in `.download/pubmed-daily/<WEEK>/`, use the `parse_pubmed_articleSet` tool to convert it to an Excel file.
-
-**Tool invocation pattern:**
-
-```
-parse_pubmed_articleSet 
-  filePath="<working_dir>/.download/pubmed-daily/<WEEK>/<filename>.xml.gz"
-  outputMode="excel"
-  outputFileName="<filename>.xlsx"
-  outputDir="<working_dir>/.download/pubmed-daily/<WEEK>"
-```
-
-**Example:**
-For file `pubmed24n1234.xml.gz` in week `20250217-20250223`:
-- Input: `.download/pubmed-daily/20250217-20250223/pubmed24n1234.xml.gz`
-- Output: `.download/pubmed-daily/20250217-20250223/pubmed24n1234.xlsx`
-
-**Process:**
-1. List all `.xml.gz` files in the week directory
-2. For each file, call `parse_pubmed_articleSet` with `outputMode="excel"`
-3. The output Excel file will be saved in the same directory as the input
-4. Report parsing statistics (articles processed, any errors)
-
-### Step 8: Combine Individual Excel Files
-
-After all individual Excel files are created, combine them into a single `combined.xlsx` file using the Python script.
-
-Extract the full path to `pubmed_weekly.py` from the `<skill_files>` section.
-
-**For Unix-like shells (Git Bash / macOS / Linux):**
-```bash
-uv run python <skill_path>/pubmed_weekly.py combine_excel "<WEEK>"
-```
-
-**For Windows cmd.exe:**
-```bash
-uv.exe run python <skill_path>\pubmed_weekly.py combine_excel "<WEEK>"
-```
-
-Where:
-- `<skill_path>` is the full directory path extracted from `<skill_files>`
-- `<WEEK>` is the actual week folder name (e.g., `20250217-20250223`)
-
-**Expected behavior:**
-- Finds all `.xlsx` files in the week directory (excluding `combined.xlsx`)
-- Reads each file and combines all rows
-- Writes `combined.xlsx` with all articles from all files
-- Returns summary: total rows, source files processed
-
-**Output location:**
-`.download/pubmed-daily/<WEEK>/combined.xlsx`
-
-## Python Script Details
-
-The skill includes a bundled Python script at `pubmed_weekly.py` with the following functions:
-
-### 1. `calculate_week()` - Calculate week date range
-
-Returns week folder name in format `YYYYMMDD-YYYYMMDD` for the past week (Monday-Sunday).
-
-### 2. `fetch_files()` - Fetch FTP file list
-
-Returns list of all xml.gz filenames from NCBI FTP server.
-
-### 3. `filter_files(week_name, file_list)` - Filter files for the week
-
-Parameters:
-- `week_name`: Week folder name (e.g., `20250217-20250223`)
-- `file_list`: List of filenames from FTP server
-
-Returns: Space-separated list of xml.gz files that fall within the date range.
-
-### 4. `download_file(week_name, filename)` - Download single file with retry
-
-Parameters:
-- `week_name`: Week folder name
-- `filename`: XML.gz filename to download
-
-Behavior:
-- Downloads from `ftp://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/<filename>`
-- Saves to `.download/pubmed-daily/<week_name>/<filename>` in current working directory
-- Creates directory structure if needed
-- Retries up to 3 times on failure
-- Returns exit code 0 on success, 1 on failure (after all retries)
-
-### 5. `combine_excel(week_name)` - Combine Excel files into combined.xlsx
-
-Parameters:
-- `week_name`: Week folder name (e.g., `20250217-20250223`)
-
-Behavior:
-- Searches for all `.xlsx` files in `.download/pubmed-daily/<week_name>/` in current working directory
-- Excludes `combined.xlsx` from the list
-- Reads each Excel file and combines all rows
-- Creates `combined.xlsx` with all articles merged
-- Returns JSON with: success, total_rows, source_files, output_file
-
-## Output Summary
-
-After completion, provide the user with:
-
-1. Week date range processed
-2. Number of files found for the week
-3. Number of files successfully downloaded
-4. Number of files failed to download (if any)
-5. Download location: `.download/pubmed-daily/<WEEK>/`
-6. Number of XML files parsed to Excel (Step 7)
-7. Total articles in combined.xlsx (Step 8)
-8. Combined file location: `.download/pubmed-daily/<WEEK>/combined.xlsx`
-
-## Notes
-
-- This skill automatically checks for and installs uv using the `python-setup-uv` skill if not present
-- The Python script is bundled with this skill at `pubmed_weekly.py`
-- All Python commands use the full script path extracted from `<skill_files>` section
-- The script uses `os.getcwd()` to determine the working directory, which is naturally the opencode working directory
-- All output files (downloads, Excel files) are created in the opencode working directory
-- The FTP server path is: `ftp://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/`
-- Only `.xml.gz` files are downloaded
-- Downloads are sequential (one file at a time)
-- Retry logic includes 2-second delays between attempts
-- User has control to abort on persistent failures
-- The script uses Python's built-in `urllib.request` for FTP operations
-- The `combine_excel` command requires `openpyxl` package (auto-installed via uv)
-- Skill directory path is extracted from `<skill_files>` section for script location
-- Windows with Git Bash: Follow Unix-like shell instructions
-- Windows cmd.exe: Use `uv.exe run python` syntax
-- Step 7 uses the `parse_pubmed_articleSet` tool for XML to Excel conversion
-- Step 8 combines all individual Excel files into a single `combined.xlsx`
+---
+name: pubmed-weekly
+description: Download PubMed daily update xml.gz files from the past week from NCBI FTP server
+allowedTools:
+  - Bash
+  - Read
+  - Write
+  - Question
+  - parse_pubmed_articleSet
+---
+
+# PubMed Weekly Daily Updates Download
+
+This skill downloads PubMed daily update xml.gz files from the past week (Monday-Sunday).
+
+## Workflow Overview
+
+1. **Python Environment Setup** (automatic): Checks for uv, installs via `python-setup-uv` skill if needed
+2. **Date Calculation**: Calculates the past week's date range (Monday-Sunday)
+3. **FTP Listing**: Fetches available xml.gz files from NCBI FTP server
+4. **Filtering**: Filters files to include only those from the past week
+5. **Download**: Downloads filtered files with retry logic (max 3 attempts per file)
+
+## Prerequisites
+- Internet connection
+- Access to NCBI FTP server
+- uv package manager (will be automatically installed if not present)
+
+## Integration with python-setup-uv
+
+This skill integrates with the `python-setup-uv` skill to ensure Python environment is properly configured.
+
+### Prerequisite Check
+
+Before starting the download process:
+
+1. **Check if uv is installed:**
+    ```bash
+    if [ -f "uv" ] || [ -f "uv.exe" ]; then
+      echo "uv already installed"
+    else
+      echo "uv not found, setting up..."
+    fi
+    ```
+
+2. **If uv is not installed:**
+   - Load the `python-setup-uv` skill using the skill tool
+   - Follow all steps EXACTLY as specified in the python-setup-uv skill
+   - Wait for uv installation to complete
+   - Continue with this skill's Step 1 below
+
+3. **After uv is installed:**
+   - The bundled script `pubmed_weekly.py` will be executed using uv
+   - Extract the full script path from the `<skill_files>` section in skill tool output
+
+## Steps
+
+Follow these steps EXACTLY as described.
+
+### Step 1: Calculate Week Date Range
+
+First, determine the date range for the past week (Monday through Sunday).
+
+Extract the full path to `pubmed_weekly.py` from the `<skill_files>` section in the skill tool output.
+
+**For Unix-like shells (Git Bash / macOS / Linux):**
+```bash
+uv run python <skill_path>/pubmed_weekly.py calculate_week
+```
+
+### Step 1: Calculate Week Date Range
+
+First, determine the date range for the past week (Monday through Sunday).
+
+Extract the full path to `pubmed_weekly.py` from the `<skill_files>` section in the skill tool output.
+
+### Step 1: Calculate Week Date Range
+
+First, determine the date range for the past week (Monday through Sunday).
+
+**For Unix-like shells (Git Bash / macOS / Linux):**
+```bash
+uv run python <skill_path>/pubmed_weekly.py calculate_week
+```
+
+**For Windows cmd.exe:**
+```bash
+uv.exe run python <skill_path>\pubmed_weekly.py calculate_week
+```
+
+Replace `<skill_path>` with the full directory path extracted from `<skill_files>`.
+
+This will output the week folder name in format `YYYYMMDD-YYYYMMDD`.
+
+**Expected output format:**
+```
+20250217-20250223
+```
+
+### Step 2: Create Download Directory
+
+The `download_file` command will automatically create the directory structure when needed. No manual directory creation is required.
+
+### Step 3: Fetch FTP File List
+
+Extract the full path to `pubmed_weekly.py` from the `<skill_files>` section and fetch the list of files from the NCBI FTP server.
+
+**For Unix-like shells:**
+```bash
+uv run python <skill_path>/pubmed_weekly.py fetch_files
+```
+
+**For Windows cmd.exe:**
+```bash
+uv.exe run python <skill_path>\pubmed_weekly.py fetch_files
+```
+
+Replace `<skill_path>` with the full directory path extracted from `<skill_files>`.
+
+This will list all daily update xml.gz files available on the FTP server.
+
+**Expected output:**
+```
+pubmed24n1234.xml.gz pubmed24n1235.xml.gz pubmed24n1236.xml.gz
+```
+
+### Step 4: Filter Files for Past Week
+
+Extract the full path to `pubmed_weekly.py` from the `<skill_files>` section and filter the file list for the past week's daily updates.
+
+**For Unix-like shells:**
+```bash
+uv run python <skill_path>/pubmed_weekly.py filter_files "<WEEK>" "<FILE_LIST>"
+```
+
+**For Windows cmd.exe:**
+```bash
+uv.exe run python <skill_path>\pubmed_weekly.py filter_files "<WEEK>" "<FILE_LIST>"
+```
+
+Where:
+- `<skill_path>` is the full directory path extracted from `<skill_files>`
+- `<WEEK>` is the week folder name (e.g., `20250217-20250223`)
+- `<FILE_LIST>` is the output from Step 3 (space-separated filenames, use quotes)
+
+This will return a space-separated list of xml.gz files from the past week.
+
+**Expected output:**
+```
+pubmed24n1234.xml.gz pubmed24n1235.xml.gz pubmed24n1236.xml.gz
+```
+
+### Step 5: Download Files with Retry
+
+Extract the full path to `pubmed_weekly.py` from the `<skill_files>` section and for each file in the filtered list, download to the target directory with retry logic.
+
+**For Unix-like shells:**
+```bash
+for file in <FILE_LIST>; do
+  uv run python <skill_path>/pubmed_weekly.py download_file <WEEK> $file
+done
+```
+
+**For Windows cmd.exe:**
+```bash
+for %f in (<FILE_LIST>) do uv.exe run python <skill_path>\pubmed_weekly.py download_file <WEEK> %f
+```
+
+Where:
+- `<skill_path>` is the full directory path extracted from `<skill_files>`
+- `<FILE_LIST>` is the space-separated list from Step 4
+- `<WEEK>` is the week folder name
+
+Replace `<FILE_LIST>` with the space-separated list from Step 4.
+
+**Download behavior:**
+- Downloads one file at a time
+- Retries up to 3 times if download fails
+- Waits 2 seconds between retry attempts
+- After 3 failed attempts, asks user whether to abort
+
+**If a download fails after 3 retries:**
+Use the question tool to ask:
+- "Abort remaining downloads?" (options: "Yes" / "No")
+
+If user selects "Yes", stop the process and report summary.
+If user selects "No", skip the failed file and continue with the next one.
+
+### Step 6: Verify Downloads
+
+After all downloads complete (or are aborted), verify the downloaded files:
+
+```bash
+ls -lh .download/pubmed-daily/<WEEK>/
+```
+
+Count the number of files downloaded and report the summary to the user.
+
+### Step 7: Parse XML Files to Individual Excel Sheets
+
+For each downloaded `.xml.gz` file in `.download/pubmed-daily/<WEEK>/`, use the `parse_pubmed_articleSet` tool to convert it to an Excel file.
+
+**Tool invocation pattern:**
+
+```
+parse_pubmed_articleSet 
+  filePath="<working_dir>/.download/pubmed-daily/<WEEK>/<filename>.xml.gz"
+  outputMode="excel"
+  outputFileName="<filename>.xlsx"
+  outputDir="<working_dir>/.download/pubmed-daily/<WEEK>"
+```
+
+**Example:**
+For file `pubmed24n1234.xml.gz` in week `20250217-20250223`:
+- Input: `.download/pubmed-daily/20250217-20250223/pubmed24n1234.xml.gz`
+- Output: `.download/pubmed-daily/20250217-20250223/pubmed24n1234.xlsx`
+
+**Process:**
+1. List all `.xml.gz` files in the week directory
+2. For each file, call `parse_pubmed_articleSet` with `outputMode="excel"`
+3. The output Excel file will be saved in the same directory as the input
+4. Report parsing statistics (articles processed, any errors)
+
+### Step 8: Combine Individual Excel Files
+
+After all individual Excel files are created, combine them into a single `combined.xlsx` file using the Python script.
+
+Extract the full path to `pubmed_weekly.py` from the `<skill_files>` section.
+
+**For Unix-like shells (Git Bash / macOS / Linux):**
+```bash
+uv run python <skill_path>/pubmed_weekly.py combine_excel "<WEEK>"
+```
+
+**For Windows cmd.exe:**
+```bash
+uv.exe run python <skill_path>\pubmed_weekly.py combine_excel "<WEEK>"
+```
+
+Where:
+- `<skill_path>` is the full directory path extracted from `<skill_files>`
+- `<WEEK>` is the actual week folder name (e.g., `20250217-20250223`)
+
+**Expected behavior:**
+- Finds all `.xlsx` files in the week directory (excluding `combined.xlsx`)
+- Reads each file and combines all rows
+- Writes `combined.xlsx` with all articles from all files
+- Returns summary: total rows, source files processed
+
+**Output location:**
+`.download/pubmed-daily/<WEEK>/combined.xlsx`
+
+## Python Script Details
+
+The skill includes a bundled Python script at `pubmed_weekly.py` with the following functions:
+
+### 1. `calculate_week()` - Calculate week date range
+
+Returns week folder name in format `YYYYMMDD-YYYYMMDD` for the past week (Monday-Sunday).
+
+### 2. `fetch_files()` - Fetch FTP file list
+
+Returns list of all xml.gz filenames from NCBI FTP server.
+
+### 3. `filter_files(week_name, file_list)` - Filter files for the week
+
+Parameters:
+- `week_name`: Week folder name (e.g., `20250217-20250223`)
+- `file_list`: List of filenames from FTP server
+
+Returns: Space-separated list of xml.gz files that fall within the date range.
+
+### 4. `download_file(week_name, filename)` - Download single file with retry
+
+Parameters:
+- `week_name`: Week folder name
+- `filename`: XML.gz filename to download
+
+Behavior:
+- Downloads from `ftp://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/<filename>`
+- Saves to `.download/pubmed-daily/<week_name>/<filename>` in current working directory
+- Creates directory structure if needed
+- Retries up to 3 times on failure
+- Returns exit code 0 on success, 1 on failure (after all retries)
+
+### 5. `combine_excel(week_name)` - Combine Excel files into combined.xlsx
+
+Parameters:
+- `week_name`: Week folder name (e.g., `20250217-20250223`)
+
+Behavior:
+- Searches for all `.xlsx` files in `.download/pubmed-daily/<week_name>/` in current working directory
+- Excludes `combined.xlsx` from the list
+- Reads each Excel file and combines all rows
+- Creates `combined.xlsx` with all articles merged
+- Returns JSON with: success, total_rows, source_files, output_file
+
+## Output Summary
+
+After completion, provide the user with:
+
+1. Week date range processed
+2. Number of files found for the week
+3. Number of files successfully downloaded
+4. Number of files failed to download (if any)
+5. Download location: `.download/pubmed-daily/<WEEK>/`
+6. Number of XML files parsed to Excel (Step 7)
+7. Total articles in combined.xlsx (Step 8)
+8. Combined file location: `.download/pubmed-daily/<WEEK>/combined.xlsx`
+
+## Notes
+
+- This skill automatically checks for and installs uv using the `python-setup-uv` skill if not present
+- The Python script is bundled with this skill at `pubmed_weekly.py`
+- All Python commands use the full script path extracted from `<skill_files>` section
+- The script uses `os.getcwd()` to determine the working directory, which is naturally the opencode working directory
+- All output files (downloads, Excel files) are created in the opencode working directory
+- The FTP server path is: `ftp://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/`
+- Only `.xml.gz` files are downloaded
+- Downloads are sequential (one file at a time)
+- Retry logic includes 2-second delays between attempts
+- User has control to abort on persistent failures
+- The script uses Python's built-in `urllib.request` for FTP operations
+- The `combine_excel` command requires `openpyxl` package (auto-installed via uv)
+- Skill directory path is extracted from `<skill_files>` section for script location
+- Windows with Git Bash: Follow Unix-like shell instructions
+- Windows cmd.exe: Use `uv.exe run python` syntax
+- Step 7 uses the `parse_pubmed_articleSet` tool for XML to Excel conversion
+- Step 8 combines all individual Excel files into a single `combined.xlsx`