Run app.py for running the Web App.

Runs main.py using subprocess.

app.py

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+from flask import Flask, request, render_template, jsonify
+from flask_mail import Mail, Message
+import subprocess
+import tempfile
+import os
+import zipfile
+import threading
+import uuid
+
+app = Flask(__name__)
+
+# Flask-Mail Configuration using fastmail's smtp server.
+app.config["MAIL_SERVER"] = "smtp.fastmail.com"
+app.config["MAIL_PORT"] = 465
+app.config["MAIL_USERNAME"] = "[email protected]"
+app.config["MAIL_PASSWORD"] = "mlc3s3x3uucdduu6" 
+app.config["MAIL_USE_TLS"] = False
+app.config["MAIL_USE_SSL"] = True
+app.config["MAIL_DEFAULT_SENDER"] = "[email protected]"
+
+mail = Mail(app)
+
+# Dictionary to store the status and output of each task.
+tasks_status = {}
+
+# Function to zip directories -- zipped output emailed.
+def zip_directories(directories, zip_filename):
+    with zipfile.ZipFile(zip_filename, 'w', zipfile.ZIP_DEFLATED) as zipf:
+        for directory in directories:
+            for root, dirs, files in os.walk(directory):
+                for file in files:
+                    file_path = os.path.join(root, file)
+                    zipf.write(file_path, os.path.relpath(file_path, os.path.join(directory, '..')))
+
+def run_command(fasta_sequence, reference_genome, email_address, task_id):
+    with tempfile.NamedTemporaryFile(delete=False, mode='w+', suffix='.fasta') as tmpfile:
+        tmpfile.write(fasta_sequence)
+        fasta_file_path = tmpfile.name
+
+    tasks_status[task_id] = {'status': 'running', 'output': ''}
+
+    # Running the main.py -- runs the entire command line mechanism.
+    command = ['python3', 'main.py', fasta_file_path, reference_genome]
+    process = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, text=True)
+
+    # Capturing output in real-time.
+    while True:
+        line = process.stdout.readline()
+        if not line and process.poll() is not None:
+            break
+        tasks_status[task_id]['output'] += line
+        print(line, end='')  # Also prints to command line
+
+    # Once command completes, email is sent.
+    try:
+        zip_filename = 'outputs.zip'
+        zip_directories(['fullSequence-output', 'geneAnalysis-output', 'avg_mutation_rate_final'], zip_filename)
+
+        with app.app_context():  # Subject and recipient for sending email.
+            msg = Message("ViralGeneClock Outputs", recipients=[email_address])
+            msg.body = "Your ViralGeneClock analysis is complete! Please find the results attached with this email."
+            with open(zip_filename, "rb") as fp:
+                msg.attach(zip_filename, "application/zip", fp.read())
+            mail.send(msg)
+
+        tasks_status[task_id]['status'] = 'emailed'
+        os.remove(zip_filename)
+    except Exception as e: # exception not working here; email sent either way. Javascript in running.html used to notify user of input failure.
+        tasks_status[task_id]['status'] = 'failed'
+        tasks_status[task_id]['output'] = str(e)
+    finally:
+        os.unlink(fasta_file_path)
+
+@app.route('/')
+def home():
+    return render_template('index.html')
+
+@app.route('/run', methods=['POST'])
+def run_script():
+    fasta_sequence = request.form['fasta_sequence']
+    reference_genome = request.form['reference_genome']
+    email_address = request.form['email']
+    task_id = str(uuid.uuid4())
+    tasks_status[task_id] = {'status': 'initialized', 'output': ''}
+
+    thread = threading.Thread(target=run_command, args=(fasta_sequence, reference_genome, email_address, task_id))
+    thread.start()
+
+    return render_template('running.html', task_id=task_id)
+
+@app.route('/status/<task_id>')
+def task_status(task_id):
+    return jsonify(tasks_status.get(task_id, {'status': 'unknown', 'output': ''}))
+
+if __name__ == '__main__':
+    app.run(debug=True)
+