Added serving and automatic rendering functionallity

.gitignore

@@ -8,3 +8,4 @@ to-do.md
 /.quarto/
 .DS_Store
 [0-9]*/
+venv/

Dockerfile

@@ -16,13 +16,15 @@ RUN apt-get update -y \
   libopenblas-base \
   libgdal-dev \
   curl \
+  python3-pip \
   && wget https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb \
   && apt-get install -y ./google-chrome-stable_current_amd64.deb \
   && rm -rf ./google-chrome-stable_current_amd64.deb \
   && curl -o quarto-linux-amd64.deb -L https://github.com/quarto-dev/quarto-cli/releases/download/v${QUARTO_VERSION}/quarto-${QUARTO_VERSION}-linux-amd64.deb \
   && apt-get install -y ./quarto-linux-amd64.deb \
   && rm -rf ./quarto-linux-amd64.deb \
   && Rscript -e 'install.packages(c("remotes","fontawesome","here","htmlTable","leaflet","readxl","writexl"),repos = "http://cran.us.r-project.org");' \
+  && pip3 install --no-cache-dir Flask==2.2.2 Werkzeug==2.2.2 PyYAML==6.0.2 watchdog==5.0.3 \
   && rm -rf /var/lib/apt/lists/* \
   && mkdir /qmd /.cache \
   && chmod 777 /qmd /.cache

README.md

@@ -77,6 +77,15 @@ docker run --rm --platform linux/amd64 -u $(id -u):$(id -g) -v ${PWD}:/qmd ghcr.
 docker run --rm --platform linux/amd64 -u $(id -u):$(id -g) -v ${PWD}:/qmd ghcr.io/nbisweden/workshop-ngsintro:latest quarto render index.qmd
 ```
 
+## Serving and automatic rendering
+
+You can use a Flask server to serve the site, and handle automatic rebuilding of pages when any `.qmd` file is changed. The browser has to be refreshed manually though.
+
+```bash
+# serve the site
+docker run --rm --platform linux/amd64 -u $(id -u):$(id -g) -v ${PWD}:/qmd -p 5000:5000  ghcr.io/nbisweden/workshop-ngsintro:latest python3 serve_quarto.py
+```
+
 ## Test scripts
 
 This is regarding the directory **scripts**. This directory contains shell scripts for reseq (variant-calling) and rnaseq parts of the workshop. These are intended to be run on UPPMAX. Further instructions on using them are available within the scripts.

serve_quarto.py

@@ -0,0 +1,66 @@
+from flask import Flask, send_from_directory
+import os
+import subprocess
+import yaml
+from watchdog.observers import Observer
+from watchdog.events import FileSystemEventHandler
+import time
+
+app = Flask(__name__)
+quarto_yml_path = '_quarto.yml'
+watched_folder = '.'
+
+# Function to read the output directory from _quarto.yml
+def read_output_dir_from_quarto_yml(quarto_yml_path):
+    with open(quarto_yml_path, 'r') as file:
+        quarto_config = yaml.safe_load(file)
+    return quarto_config.get('project', {}).get('output-dir', 'default-output-folder')
+
+output_folder = read_output_dir_from_quarto_yml(quarto_yml_path)
+
+class QuartoHandler(FileSystemEventHandler):
+    def __init__(self):
+        self.last_modified_time = {}
+
+    def should_process(self, file_path, cooldown=2):
+        # Check the time of the last modification for the given file
+        last_time = self.last_modified_time.get(file_path, 0)
+        # Get the current time
+        current_time = time.time()
+        # If the last modification was more recent than the cooldown, skip processing
+        if current_time - last_time < cooldown:
+            return False
+        # Update the last modification time and proceed
+        self.last_modified_time[file_path] = current_time
+        return True
+
+    def on_modified(self, event):
+        if not event.is_directory and event.src_path.endswith('.qmd'):
+            if self.should_process(event.src_path):
+                print(f"Detected changes in {event.src_path}. Rendering...")
+                # Run the Quarto render command for the specific file
+                subprocess.run(['quarto', 'render', event.src_path])
+
+
+# Set up file watcher
+event_handler = QuartoHandler()
+observer = Observer()
+observer.schedule(event_handler, watched_folder, recursive=True)
+observer.start()
+
+
+@app.route('/')
+def index():
+    # Serve the index.html file
+    return send_from_directory(output_folder, 'index.html')
+
+@app.route('/<path:filename>')
+def serve_file(filename):
+    # Serve the rendered file
+    return send_from_directory(output_folder, filename)
+
+
+if __name__ == '__main__':
+    output_folder = read_output_dir_from_quarto_yml(quarto_yml_path)  # Update the output folder on the startup
+    app.run(host='0.0.0.0', port=5000, debug=True)
+