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author itaxotools
date Sun, 29 Jan 2023 16:25:48 +0000
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1 #!/usr/bin/env python
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2 # -*- coding: utf-8 -*-
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3
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4 from flask import Flask, make_response, request, current_app, send_file, url_for
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5 from flask_restful import Resource, Api, reqparse, abort
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6 from flask.json import jsonify
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7 from flasgger import Swagger
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8 from flask_cors import CORS, cross_origin
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9 from flask_restful.utils import cors
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10 import logging
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11 import base64
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12 import uuid
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13 import tempfile
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14 import os
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15 import html2text
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16
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17 # for emails
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18 import smtplib
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19 from email.message import EmailMessage
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20 from email.mime.multipart import MIMEMultipart
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21 from email.mime.text import MIMEText
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22 from email.mime.image import MIMEImage
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23 from celery import Celery
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24 from celery.schedules import crontab
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25
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26 import json
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27
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28 #from MolD_sDNC import SortedDisplayDict
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29 #from MolD_sDNC import Step1
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30 #from MolD_sDNC import C_VP_PP
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31 #from MolD_sDNC import random_position
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32 #from MolD_sDNC import step_reduction_complist
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33 #from MolD_sDNC import ConditionD
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34 #from MolD_sDNC import RemoveRedundantPositions
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35 #from MolD_sDNC import Diagnostic_combinations
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36 #from MolD_sDNC import IndependentKey
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37 #from MolD_sDNC import random_sequence2
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38 #from MolD_sDNC import GenerateBarcode2
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39 #from MolD_sDNC import Screwed_dataset31
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40 from MolD_sDNCFASTA import mainprocessing
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41
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42
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43 logging.basicConfig(format='%(levelname)s: %(asctime)s - %(message)s',
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44 level=logging.DEBUG, datefmt='%d.%m.%Y %I:%M:%S %p')
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45
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46 app = Flask(__name__)
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47 app.config.from_envvar('APPSETTINGS')
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48 API_VERSION = app.config.get('API_VERSION', 1)
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49
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50 cors = CORS(app, resources={r"/*": {"origins": "*"}}, methods=['GET', 'POST', 'PATCH', 'DELETE', 'HEAD', 'OPTIONS'])
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51 api = Api(app, prefix=f"/api/v{API_VERSION}")
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52
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53 gunicorn_logger = logging.getLogger('gunicorn.error')
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54 app.logger.handlers = gunicorn_logger.handlers
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55 app.logger.setLevel(gunicorn_logger.level)
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56
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57 REDIS_HOST = app.config.get('REDIS_HOST', 'localhost')
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58 REDIS_PORT = app.config.get('REDIS_PORT', 6379)
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59 REDIS_DB = app.config.get('REDIS_DB', 0)
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60
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61 MAILUSER = app.config.get('MAILUSER')
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62 MAILPASS = app.config.get('MAILPASS')
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63
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64 app.config['SWAGGER'] = {
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65 'uiversion': 3
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66 }
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67 swtemplate = {
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68 "info": {
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69 "title": "MoID API",
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70 "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",
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71 "version": f"{API_VERSION}",
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72 },
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73 "schemes": [
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74 "https"
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75 ]
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76 }
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77
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78 swagger_config = {
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79 "headers": [
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80 ],
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81 "specs": [
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82 {
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83 "endpoint": 'apidescr',
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84 "route": '/apidescr.json',
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85 "rule_filter": lambda rule: True,
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86 "model_filter": lambda tag: True,
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87 }
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88 ],
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89 "static_url_path": "/flasgger_static",
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90 "swagger_ui": True,
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91 "specs_route": "/docs/",
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92 'uiversion': 3
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93 }
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94
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95 swagger = Swagger(app, config=swagger_config, template=swtemplate)
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96
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97 SEND_EMAILS = True
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98
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99 app.config['CELERY_BROKER_URL'] = 'redis://{}:{}/{}'.format(REDIS_HOST, REDIS_PORT, REDIS_DB)
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100 app.config['CELERY_RESULT_BACKEND'] = 'redis://{}:{}/{}'.format(REDIS_HOST, REDIS_PORT, REDIS_DB)
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101
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102 def make_celery(app):
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103 celery = Celery(app.import_name, broker=app.config['CELERY_BROKER_URL'])
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104 celery.conf.update(app.config)
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105 TaskBase = celery.Task
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106 class ContextTask(TaskBase):
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107 abstract = True
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108 def __call__(self, *args, **kwargs):
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109 with app.app_context():
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110 return TaskBase.__call__(self, *args, **kwargs)
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111 celery.Task = ContextTask
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112 return celery
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113
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114 celery = make_celery(app)
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115
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116 #@celery.on_after_configure.connect
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117 #def setup_periodic_tasks(sender, **kwargs):
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118 # sender.add_periodic_task(
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119 # crontab(minute=0, hour='*/3'),
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120 # check_pending_notifications.s(),
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121 # )
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122
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123
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124 @celery.task
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125 def send_email_notification(email, status, parameters, taxalist, orig_filename):
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126 print("Sending email")
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127 sender = MAILUSER
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128 taxa = ", ".join(taxalist)
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129 print(taxalist)
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130 taxa1 = "-".join([t.replace(" ", "_") for t in taxalist])
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131 msg = MIMEMultipart('related')
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132 msg['Subject'] = f'MolD results: {taxa}'
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133 msg['From'] = sender
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134 msg['To'] = email
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135
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136 # TODO: add three txt files:
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137 #
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138
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139 email_body = """\
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140 <html>
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141 <head></head>
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142 <body>
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143
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144 Results:
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145 {}
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146
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147 ***************
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148
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149 <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>
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150 </body>
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151 </html>
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152 """.format(status)
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153
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154 plain_text_results = html2text.html2text(status)
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155
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156 message_text = MIMEText(email_body, 'html')
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157 msg.attach(message_text)
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158
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159 text_attachment = f"""
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160 Results:
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161 {plain_text_results}
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162
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163 ***************
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164
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165 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
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166 """
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167
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168 mail_attachment = MIMEText(text_attachment)
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169 fname = f"{orig_filename}.results.txt"
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170 mail_attachment.add_header('Content-Disposition', 'attachment', filename=fname)
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171 msg.attach(mail_attachment)
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172
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173 print("mail ready to be sent")
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174 s = smtplib.SMTP('smtp.gmail.com', 587)
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175 s.ehlo()
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176 s.starttls()
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177 s.login(MAILUSER, MAILPASS)
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178 s.sendmail(sender, email, msg.as_string())
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179 s.quit()
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180 print("mail sent")
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181
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182
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183 @celery.task
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184 def process_data(email, gapsaschars, taxalist, taxonrank, cutoff, numnucl, numiter, maxlenraw, maxlenrefined, pdiff, nmax, thresh, tmpfname, orig_fname):
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185 print("Processing data")
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186
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187 results, qclades = mainprocessing(gapsaschars, taxalist, taxonrank, cutoff, numnucl, numiter, maxlenraw, maxlenrefined, pdiff, nmax, thresh, tmpfname, orig_fname)
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188
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189 parameters = f"""
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190 List of focus taxa: {taxalist}
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191 Taxon rank: {taxonrank}
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192 Cutoff: {cutoff}
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193 NNNNN...: {numnucl}
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194 Num iterations: {numiter}
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195 Max length for the raw mDNCs: {maxlenraw}
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196 Max length for the refined mDNCs: {maxlenrefined}
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197 Pdiff: {pdiff}
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198 NMaxSeq: {nmax}
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199 Threshold of rDNC rating: {thresh}
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200 """
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201
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202 send_email_notification.delay(email, results, parameters, qclades, orig_fname)
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203
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204 @app.errorhandler(404)
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205 def not_found(error):
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206 return make_response(jsonify({'error': 'Not found'}), 404)
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207
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208
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209 class DataAPI(Resource):
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210 def __init__(self):
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211 self.method_decorators = []
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212
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213 def options(self, *args, **kwargs):
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214 return jsonify([])
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215
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216
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217 #@token_required
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218 @cross_origin()
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219 def post(self):
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220 """
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221 POST data to analyse
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222 ---
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223 parameters:
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224 - in: formData
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225 name: file
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226 type: file
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227 required: true
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228 description: Data file
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229 - in: formData
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230 name: tags
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231 type: array
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232 required: false
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233 description: A list of image tags to link with the image
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234 items:
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235 type: string
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236 description: Tag text
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237 - in: formData
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238 name: width
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239 type: integer
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240 required: false
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241 description: Image width
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242 - in: formData
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243 name: height
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244 type: integer
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245 required: false
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246 description: Image height
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247
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248 responses:
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249 200:
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250 description: Data processing
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251 400:
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252 description: Bad request
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253 """
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254 app.logger.debug(request.files)
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255 app.logger.debug(request.values)
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256 email = request.values.get('email', None)
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257 gapsaschars = request.values.get('gapsaschars', "no")
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258 taxalist = request.values.get('taxalist', "ALL")
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259 taxalist = taxalist.replace(" ", '')
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260 taxonrank = int(request.values.get('taxonrank', 2))
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261 cutoff = request.values.get('cutoff', ">0")
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262 numnucl = int(request.values.get('numnucl', 5))
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263 numiter = int(request.values.get('numites', 10000))
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264 maxlenraw = int(request.values.get('maxlenraw', 12))
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265 maxlenrefined = int(request.values.get('maxlenrefined', 7))
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266 pdiff = int(request.values.get('pdiff', 1))
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267 #prseq = float(request.values.get('prseq', 0.1))
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268 nmax = int(request.values.get('nmax', 20))
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269 thresh = int(request.values.get('thresh', 85))
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270
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271 if not all([email, gapsaschars, taxalist, taxonrank, cutoff, numnucl, numiter, maxlenraw, maxlenrefined, pdiff, nmax, thresh]):
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272 return make_response(jsonify({'error': 'Parameter missing'}), 400)
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273
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274 if not request.files:
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275 return make_response(jsonify({'error': 'No file provided'}), 400)
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276
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277
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278 data_file = [request.files.get(f) for f in request.files][-1]
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279
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280 thumb_height = request.values.get('height', None)
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281 tmpdname = "/tmp"
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282 tmpfname = str(uuid.uuid4())
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283 tmp_upl_file = os.path.join(tmpdname, tmpfname)
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284 data_file.save(tmp_upl_file)
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285 app.logger.debug(tmp_upl_file)
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286 process_data.delay(email, gapsaschars, taxalist, taxonrank, cutoff, numnucl, numiter, maxlenraw, maxlenrefined, pdiff, nmax, thresh, tmp_upl_file, data_file.filename)
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287
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288 return jsonify("OK"), 200
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289
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290
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291 api.add_resource(DataAPI, '/data', endpoint='processdata')
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292
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293 if __name__ == '__main__':
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294 app.debug = True
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295 app.run(host='0.0.0.0')