Add mail send at the end of a job

application.properties.example

@@ -4,9 +4,16 @@ data_folder = ###PROGRAM###/data
 # batch system type: local, sge, slurm
 batch_system_type = local
 threads = 4
+web_url = http://localhost:5000
 
 [softwares]
 minimap2 = ###DEFAULT###
 
 [database]
 sqlite_file = ###PROGRAM###/srv/database.sqlite
+
+[mail]
+status = mail@dgenies
+reply = mail@dgenies
+org = "Dgenies team"
+send_mail_status = True
\ No newline at end of file

lib/job_manager.py

@@ -12,11 +12,13 @@ from lib.Fasta import Fasta
 from lib.functions import Functions
 import requests
 import wget
+from jinja2 import Template
+from flask_mail import Message
 
 
 class JobManager:
 
-    def __init__(self, id_job: str, email: str=None, query: Fasta=None, target: Fasta=None):
+    def __init__(self, id_job: str, email: str=None, query: Fasta=None, target: Fasta=None, mailer: "Mail"=None):
         self.id_job = id_job
         self.email = email
         self.query = query
@@ -27,6 +29,11 @@ class JobManager:
         self.minimap2 = config_reader.get_minimap2_exec()
         self.threads = config_reader.get_nb_threads()
         self.app_data = config_reader.get_app_data()
+        self.web_url = config_reader.get_web_url()
+        self.mail_status = config_reader.get_mail_status_sender()
+        self.mail_reply = config_reader.get_mail_reply()
+        self.mail_org = config_reader.get_mail_org()
+        self.do_send = config_reader.get_send_mail_status()
         # Outputs:
         self.output_dir = os.path.join(self.app_data, id_job)
         self.paf = os.path.join(self.output_dir, "map.paf")
@@ -34,6 +41,7 @@ class JobManager:
         self.idx_q = os.path.join(self.output_dir, "query.idx")
         self.idx_t = os.path.join(self.output_dir, "target.idx")
         self.logs = os.path.join(self.output_dir, "logs.txt")
+        self.mailer = mailer
 
     def __check_job_success_local(self):
         if os.path.exists(self.paf):
@@ -45,6 +53,50 @@ class JobManager:
         if self.batch_system_type == "local":
             return self.__check_job_success_local()
 
+    def get_mail_content(self):
+        message = "D-Genies\n\n"
+        if self.status == "success":
+            message += "Your job %s has successfully ended!\n\n" % self.id_job
+            message += str("Your job {0} is finished. You can see  the results by clicking on the link below:\n"
+                           "{1}/results/{0}\n\n").format(self.id_job, self.web_url)
+        else:
+            message += "Your job %s has failed!\n\n" % self.id_job
+            message += "Your job %s has failed. If the problem persists, please contact the support.\n\n" % self.id_job
+        message += "See you soon on D-Genies,\n"
+        message += "The team"
+
+    def get_mail_content_html(self):
+        template_str = """<h1>D-Genies</h1>
+<h3>{% if status == "success" %}Your job {{ job_name }} has successfully ended!{% else %}Your job {{ job_name }} has failed{% endif %}</h3>
+<p>Hi,</p>
+{% if status == "success" %}
+<p>Your job {{ job_name }} is finished. You can <a href="{{ url_base }}/results/{{ job_name }}">click here</a> to see results.</p>
+{% else %}
+<p>Your job {{ job_name }} has failed. If the problem persists, please contact the support.</p>
+{% endif %}
+<p>See you soon on D-Genies,</p>
+<p>The team</p>
+        """
+        template = Template(template_str)
+        return template.render(job_name=self.id_job, status=self.status, url_base=self.web_url)
+
+    def get_mail_subject(self):
+        if self.status == "success":
+            return "DGenies - Job %s finished" % self.id_job
+        else:
+            return "DGenies - Job %s failed" % self.id_job
+
+    def send_mail(self):
+        msg = Message(
+            subject=self.get_mail_subject(),
+            recipients=self.email,
+            html=self.get_mail_content_html(),
+            body=self.get_mail_content(),
+            sender=(self.mail_org, self.mail_status) if self.mail_org is not None else self.mail_status,
+            reply_to=self.mail_reply
+        )
+        self.mailer.send(msg)
+
     @db_session
     def __launch_local(self):
         cmd = ["run_minimap2.sh", self.minimap2, self.threads,
@@ -150,6 +202,8 @@ class JobManager:
                 job = Job.get(id_job=self.id_job)
                 job.status = "success"
                 db.commit()
+        if self.do_send:
+            self.send_mail()
 
     @staticmethod
     def index_file(fasta: Fasta, out):

requirements.txt

 flask==0.12.*
+Flask-Mail==0.9.*
 Jinja2==2.9.*
 pony==0.7.*
 docopt==0.6.*

srv/config_reader.py

@@ -48,6 +48,12 @@ class AppConfigReader(object):
         except NoOptionError:
             return "4"
 
+    def get_web_url(self):
+        try:
+            return self.replace_vars(self.reader.get("global", "web_url"))
+        except NoOptionError:
+            return "http://localhost:5000"
+
     def get_minimap2_exec(self):
         try:
             entry = self.reader.get("softwares", "minimap2")
@@ -60,3 +66,27 @@ class AppConfigReader(object):
             return self.replace_vars(self.reader.get("database", "sqlite_file"))
         except NoOptionError:
             return ":memory:"
+
+    def get_mail_status_sender(self):
+        try:
+            return self.replace_vars(self.reader.get("mail", "status"))
+        except NoOptionError:
+            return "status@dgenies"
+
+    def get_mail_reply(self):
+        try:
+            return self.replace_vars(self.reader.get("mail", "reply"))
+        except NoOptionError:
+            return "status@dgenies"
+
+    def get_mail_org(self):
+        try:
+            return self.replace_vars(self.reader.get("mail", "org"))
+        except NoOptionError:
+            return None
+
+    def get_send_mail_status(self):
+        try:
+            return self.replace_vars(self.reader.get("mail", "send_mail_status"))
+        except NoOptionError:
+            return False

srv/main.py

@@ -5,6 +5,7 @@ import time
 import datetime
 import shutil
 from flask import Flask, render_template, request, url_for, jsonify, session
+from flask_mail import Mail
 from lib.paf import Paf
 from config_reader import AppConfigReader
 from lib.job_manager import JobManager
@@ -33,6 +34,9 @@ app = Flask(__name__, static_url_path='/static')
 app.config['UPLOAD_FOLDER'] = UPLOAD_FOLDER
 app.config['SECRET_KEY'] = 'dsqdsq-255sdA-fHfg52-25Asd5'
 
+# Init mail:
+mail = Mail(app)
+
 # Folder containing data:
 app_data = config_reader.get_app_data()
 
@@ -110,7 +114,7 @@ def launch_analysis():
             target = Fasta(name=target_name, path=target_path, type_f=file_target_type)
 
         # Launch job:
-        job = JobManager(id_job, email, query, target)
+        job = JobManager(id_job, email, query, target, mail)
         job.launch()
         return jsonify({"success": True, "redirect": url_for(".status", id_job=id_job)})
     else: