--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/api.py	Sun Jan 29 16:25:48 2023 +0000
@@ -0,0 +1,295 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from flask import Flask, make_response, request, current_app, send_file, url_for
+from flask_restful import Resource, Api, reqparse, abort
+from flask.json import jsonify
+from flasgger import Swagger
+from flask_cors import CORS, cross_origin
+from flask_restful.utils import cors
+import logging
+import base64
+import uuid
+import tempfile
+import os
+import html2text
+
+# for emails
+import smtplib
+from email.message import EmailMessage
+from email.mime.multipart import MIMEMultipart
+from email.mime.text import MIMEText
+from email.mime.image import MIMEImage
+from celery import Celery
+from celery.schedules import crontab
+
+import json
+
+#from MolD_sDNC import SortedDisplayDict
+#from MolD_sDNC import Step1
+#from MolD_sDNC import C_VP_PP
+#from MolD_sDNC import random_position
+#from MolD_sDNC import step_reduction_complist
+#from MolD_sDNC import ConditionD
+#from MolD_sDNC import RemoveRedundantPositions
+#from MolD_sDNC import Diagnostic_combinations
+#from MolD_sDNC import IndependentKey
+#from MolD_sDNC import random_sequence2
+#from MolD_sDNC import GenerateBarcode2
+#from MolD_sDNC import Screwed_dataset31
+from MolD_sDNCFASTA import mainprocessing
+
+
+logging.basicConfig(format='%(levelname)s: %(asctime)s - %(message)s',
+                    level=logging.DEBUG, datefmt='%d.%m.%Y %I:%M:%S %p')
+
+app = Flask(__name__)
+app.config.from_envvar('APPSETTINGS')
+API_VERSION = app.config.get('API_VERSION', 1)
+
+cors = CORS(app, resources={r"/*": {"origins": "*"}}, methods=['GET', 'POST', 'PATCH', 'DELETE', 'HEAD', 'OPTIONS'])
+api = Api(app, prefix=f"/api/v{API_VERSION}")
+
+gunicorn_logger = logging.getLogger('gunicorn.error')
+app.logger.handlers = gunicorn_logger.handlers
+app.logger.setLevel(gunicorn_logger.level)
+
+REDIS_HOST = app.config.get('REDIS_HOST', 'localhost')
+REDIS_PORT = app.config.get('REDIS_PORT', 6379)
+REDIS_DB = app.config.get('REDIS_DB', 0)
+
+MAILUSER = app.config.get('MAILUSER')
+MAILPASS = app.config.get('MAILPASS')
+
+app.config['SWAGGER'] = {
+    'uiversion': 3
+}
+swtemplate = {
+    "info": {
+        "title": "MoID API",
+        "description": "MoID API is the online version of a tree independent algorithm to retrieve diagnostic nucleotide characters from monolocus datasets. BioRxiv. DOI: 10.1101/838151",
+        "version": f"{API_VERSION}",
+    },
+    "schemes": [
+        "https"
+    ]
+}
+
+swagger_config = {
+    "headers": [
+    ],
+    "specs": [
+        {
+            "endpoint": 'apidescr',
+            "route": '/apidescr.json',
+            "rule_filter": lambda rule: True,
+            "model_filter": lambda tag: True,
+        }
+    ],
+    "static_url_path": "/flasgger_static",
+    "swagger_ui": True,
+    "specs_route": "/docs/",
+    'uiversion': 3
+}
+
+swagger = Swagger(app, config=swagger_config, template=swtemplate)
+
+SEND_EMAILS = True
+
+app.config['CELERY_BROKER_URL'] = 'redis://{}:{}/{}'.format(REDIS_HOST, REDIS_PORT, REDIS_DB)
+app.config['CELERY_RESULT_BACKEND'] = 'redis://{}:{}/{}'.format(REDIS_HOST, REDIS_PORT, REDIS_DB)
+
+def make_celery(app):
+    celery = Celery(app.import_name, broker=app.config['CELERY_BROKER_URL'])
+    celery.conf.update(app.config)
+    TaskBase = celery.Task
+    class ContextTask(TaskBase):
+        abstract = True
+        def __call__(self, *args, **kwargs):
+            with app.app_context():
+                return TaskBase.__call__(self, *args, **kwargs)
+    celery.Task = ContextTask
+    return celery
+
+celery = make_celery(app)
+
+#@celery.on_after_configure.connect
+#def setup_periodic_tasks(sender, **kwargs):
+#    sender.add_periodic_task(
+#        crontab(minute=0, hour='*/3'),
+#        check_pending_notifications.s(),
+#    )
+
+
+@celery.task
+def send_email_notification(email, status, parameters, taxalist, orig_filename):
+    print("Sending email")
+    sender = MAILUSER
+    taxa = ", ".join(taxalist)
+    print(taxalist)
+    taxa1 = "-".join([t.replace(" ", "_") for t in taxalist])
+    msg = MIMEMultipart('related')
+    msg['Subject'] = f'MolD results: {taxa}'
+    msg['From'] = sender
+    msg['To'] = email
+
+    # TODO: add three txt files:
+    # 
+    
+    email_body = """\
+<html>
+    <head></head>
+       <body>
+
+    Results:
+     {}
+
+    ***************
+
+    <p>Citation: <b>Fedosov A.E.</b>, Achaz G., Puillandre N. 2019. Revisiting use of DNA characters in taxonomy with MolD – a tree independent algorithm to retrieve diagnostic nucleotide characters from monolocus datasets. BioRxiv, published online on 11.11.2019. DOI: 10.1101/838151 </p>
+       </body>
+</html>
+    """.format(status)
+    
+    plain_text_results = html2text.html2text(status)
+    
+    message_text = MIMEText(email_body, 'html')
+    msg.attach(message_text)
+
+    text_attachment = f"""
+Results: 
+{plain_text_results}
+
+***************
+
+Citation: Fedosov A.E., Achaz G., Puillandre N. 2019. Revisiting use of DNA characters in taxonomy with MolD – a tree independent algorithm to retrieve diagnostic nucleotide characters from monolocus datasets. BioRxiv, published online on 11.11.2019. DOI: 10.1101/838151
+    """
+    
+    mail_attachment = MIMEText(text_attachment)
+    fname = f"{orig_filename}.results.txt"
+    mail_attachment.add_header('Content-Disposition', 'attachment', filename=fname)
+    msg.attach(mail_attachment)
+    
+    print("mail ready to be sent")
+    s = smtplib.SMTP('smtp.gmail.com', 587)
+    s.ehlo()
+    s.starttls()
+    s.login(MAILUSER, MAILPASS)
+    s.sendmail(sender, email, msg.as_string())
+    s.quit()
+    print("mail sent")
+
+
+@celery.task
+def process_data(email, gapsaschars, taxalist, taxonrank, cutoff, numnucl, numiter, maxlenraw, maxlenrefined, pdiff, nmax, thresh, tmpfname, orig_fname):
+    print("Processing data")
+
+    results, qclades = mainprocessing(gapsaschars, taxalist, taxonrank, cutoff, numnucl, numiter, maxlenraw, maxlenrefined, pdiff, nmax, thresh, tmpfname, orig_fname)
+
+    parameters = f"""
+    List of focus taxa: {taxalist}
+    Taxon rank: {taxonrank}
+    Cutoff: {cutoff}
+    NNNNN...: {numnucl}
+    Num iterations: {numiter}
+    Max length for the raw mDNCs: {maxlenraw}
+    Max length for the refined mDNCs: {maxlenrefined}
+    Pdiff: {pdiff}
+    NMaxSeq: {nmax}
+    Threshold of rDNC rating: {thresh}
+    """
+    
+    send_email_notification.delay(email, results, parameters, qclades, orig_fname)
+    
+@app.errorhandler(404)
+def not_found(error):
+    return make_response(jsonify({'error': 'Not found'}), 404)
+
+
+class DataAPI(Resource):
+    def __init__(self):
+        self.method_decorators = []
+
+    def options(self, *args, **kwargs):
+        return jsonify([])
+
+
+    #@token_required
+    @cross_origin()
+    def post(self):
+        """
+        POST data to analyse
+        ---
+        parameters:
+         - in: formData
+           name: file
+           type: file
+           required: true
+           description: Data file
+         - in: formData
+           name: tags
+           type: array
+           required: false
+           description: A list of image tags to link with the image
+           items:
+             type: string
+             description: Tag text
+         - in: formData
+           name: width
+           type: integer
+           required: false
+           description: Image width
+         - in: formData
+           name: height
+           type: integer
+           required: false
+           description: Image height
+
+        responses:
+          200:
+            description: Data processing
+          400:
+            description: Bad request
+        """
+        app.logger.debug(request.files)
+        app.logger.debug(request.values)
+        email = request.values.get('email', None)
+        gapsaschars = request.values.get('gapsaschars', "no")
+        taxalist = request.values.get('taxalist', "ALL")
+        taxalist = taxalist.replace(" ", '')
+        taxonrank = int(request.values.get('taxonrank', 2))
+        cutoff = request.values.get('cutoff', ">0")
+        numnucl = int(request.values.get('numnucl', 5))
+        numiter = int(request.values.get('numites', 10000))
+        maxlenraw = int(request.values.get('maxlenraw', 12))
+        maxlenrefined = int(request.values.get('maxlenrefined', 7))
+        pdiff = int(request.values.get('pdiff', 1))
+        #prseq = float(request.values.get('prseq', 0.1))
+        nmax = int(request.values.get('nmax', 20))
+        thresh = int(request.values.get('thresh', 85))
+        
+        if not all([email, gapsaschars, taxalist, taxonrank, cutoff, numnucl, numiter, maxlenraw, maxlenrefined, pdiff, nmax, thresh]):
+            return make_response(jsonify({'error': 'Parameter missing'}), 400)
+            
+        if not request.files:
+            return make_response(jsonify({'error': 'No file provided'}), 400)
+
+        
+        data_file = [request.files.get(f) for f in request.files][-1]
+
+        thumb_height = request.values.get('height', None)
+        tmpdname = "/tmp"
+        tmpfname = str(uuid.uuid4())
+        tmp_upl_file = os.path.join(tmpdname, tmpfname)
+        data_file.save(tmp_upl_file)
+        app.logger.debug(tmp_upl_file)
+        process_data.delay(email, gapsaschars, taxalist, taxonrank, cutoff, numnucl, numiter, maxlenraw, maxlenrefined, pdiff, nmax, thresh, tmp_upl_file, data_file.filename)
+
+        return jsonify("OK"), 200
+
+
+api.add_resource(DataAPI, '/data', endpoint='processdata')
+
+if __name__ == '__main__':
+    app.debug = True
+    app.run(host='0.0.0.0')