modify email module and star_dev

ncats · Feb 12, 2024 · cab7397 · cab7397
1 parent ecee41f
commit cab7397
Show file tree

Hide file tree

Showing 17 changed files with 516 additions and 91 deletions.
diff --git a/AlertCypher.py b/AlertCypher.py
@@ -1,3 +1,5 @@
+import sys
+# sys.path.append('/home/aom2/.conda/envs/rdas/lib/python3.8/site-packages')
 from neo4j import GraphDatabase,Auth
 from neo4j.debug import watch
 import configparser
@@ -12,6 +14,14 @@ def __init__(self, db):
         """
         Initializes the AlertCypher class.
 
+        Parameters:
+        - db (str): The name of the Neo4j database to connect to.
+        """
+
+        # Initializes the object with the config.ini file
+        """
+        Initializes the AlertCypher class.
+
         Parameters:
         - db (str): The name of the Neo4j database to connect to.
         """
@@ -22,11 +32,13 @@ def __init__(self, db):
         self.configuration = configparser.ConfigParser()
         self.configuration.read(self.init)
 
-        # Connects to Neo4j database
+        # Connects to neo4j databasej
         server_uri = os.environ['NEO4J_URI']
         user = os.environ['NEO4J_USERNAME']
         password = os.environ['NEO4J_PASSWORD']
 
+        #watch("neo4j")
+
         neo4j_auth = Auth(scheme='basic',principal=user,credentials=password)
         connection = GraphDatabase.driver(uri=server_uri, auth=neo4j_auth) 
         self.session = connection.session(database=db)

diff --git a/clinical/methods.py b/clinical/methods.py
@@ -17,7 +17,7 @@
 from selenium.webdriver.chrome.service import Service
 from selenium.webdriver.common.by import By
 from selenium.webdriver.support.ui import Select
-import spacy
+# import spacy
 import nltk
 from nltk.stem import PorterStemmer
 nltk.download("punkt")

diff --git a/config.ini b/config.ini
@@ -10,8 +10,12 @@ gard_dbname = gard
 ct_interval = 7
 pm_interval = 7
 gnt_interval = 365
-ct_update = 10/31/23
-pm_update = 11/07/23
+ct_update = 02/06/24
+pm_update = 02/01/24
+minghui.clinical_update = 01/08/24
+minghui.grant_update = 11/30/22
+minghui.pubmed_update = 10/30/22
+minghui.gard_update = 11/30/23
 
 [TEST_TRANSFER_DETECTION]
 clinical = 

diff --git a/email/alert.py → emails/alert.py b/email/alert.py → emails/alert.py
diff --git a/emails/email_template1.html b/emails/email_template1.html
@@ -0,0 +1,32 @@
+<!-- email_template.html -->
+<html>
+<head>
+    <style>
+        body { background-color: white; font-family: Arial, sans-serif; }
+        /* Add more styling as needed */
+    </style>
+</head>
+<body style="text-align: center;">
+    <h1 style="font-size:50;color:purple">Rare Disease Alert System</h1>
+    <h2>{{ name }}</h2>
+    <h3>You have {{ data['total'] }} new entries for your subscribed rare diseases in the {{ data['db_title'] }} database</h3>
+    <table border="1" style="margin: auto;">
+        <tr>
+            <th>Name</th>
+            <th>GARD ID</th>
+            <th>Nodes Modified</th>
+        </tr>
+        {% for gard_id in data['subscriptions'] %}
+            {% if data[gard_id]["num"]>0 %}
+                <tr>
+                    <td><a href="https://rdas.ncats.nih.gov/disease?id={{ gard_id }}"> {{ data[gard_id]['name'] }} </a></td>
+                    <td>{{ gard_id }}</td>
+                    <td>{{ data[gard_id]['num'] }}</td>
+                </tr>
+           {% endif %}
+        {% endfor %}
+    </table>
+    <h4>Results gathered within the time period of {{ data['update_date_start'] }} - {{ data['update_date_end'] }}</h4>
+    <img src="https://upload.wikimedia.org/wikipedia/commons/6/6e/National_Center_for_Advancing_Translational_Sciences_logo.png" alt="Rare Disease Alert System" width="300">
+</body>
+</html>
diff --git a/emails/email_test.py b/emails/email_test.py
@@ -0,0 +1,50 @@
+
+import sys
+
+sys.path.append('/home/aom2/RDAS')
+sys.path.append('/home/aom2/RDAS/emails')
+import sysvars
+import smtplib
+from email.mime.text import MIMEText
+from email.mime.multipart import MIMEMultipart
+from jinja2 import Environment, FileSystemLoader
+import os
+
+
+def send_email(subject, html, recipient):
+    print("sending emails to::", recipient)
+    sender = ""  # Replace with your email
+    password = ""  # Replace with your email password
+
+    # Set up the email
+    msg = MIMEMultipart('alternative')
+    msg['From'] = ""
+    # msg['To'] = ""
+    msg['Subject'] = subject
+
+    # Attach both plain text and HTML parts
+    # part1 = MIMEText(text, 'plain')
+    part2 = MIMEText(html, 'html')
+    # msg.attach(part1)
+    msg.attach(part2)
+
+    # Send the email
+    server = smtplib.SMTP('', 587)  # Replace with SMTP server and port
+    server.starttls()
+    server.login(sender, password)
+    text = msg.as_string()
+    server.sendmail(sender, recipient, msg.as_string())
+    server.quit()
+
+
+# def render_template(filename, data={}):
+#     # template_dir = "path/to/templates"
+#     template_dir = os.getcwd()
+#     env = Environment(loader=FileSystemLoader(template_dir))
+#     template_path = filename  # Relative to the template_dir
+#     template = env.get_template(template_path)
+#     return template.render(data=data)
+
+# the fill_template method was remove, becaus the generation of message was integrated into the html template.
+
+
diff --git a/emails/ses_firebase.py b/emails/ses_firebase.py
@@ -0,0 +1,169 @@
+import glob
+import os
+import sys
+workspace = os.path.dirname(os.path.abspath(__file__))
+sys.path.append(workspace)
+sys.path.append(os.getcwd())
+import sysvars
+from AlertCypher import AlertCypher
+from datetime import date,datetime
+import pandas as pd
+from dateutil.relativedelta import relativedelta
+import firebase_admin
+from firebase_admin import auth
+from firebase_admin import credentials
+from firebase_admin import firestore
+import alert
+def fill_template(type,data):
+    tabs = {'clinical':'trials', 'grant':'project', 'pubmed':'nonepi-articles'}
+    txt_db = {'clinical': 'clinical trial', 'grant': 'funded project', 'pubmed': 'publication'}
+    full_msg = ''
+    html = ''
+
+    full_msg += 'You have {num} new entries for your subscribed rare diseases in the {db_title} database\nOut of that {num},\n\n'.format(num=data['total'], db_title=txt_db[type])
+
+    html += """
+        <html>
+        <head>
+        </head>
+        <body style="background-color:white;font-family: Arial, sans-serif;">
+        <div style="text-align:center">
+        <h1 style="font-size:50;color:purple"><u>Rare Disease Alert System</u></h1>
+        </div>
+        <div style="text-align:center;margin:auto">
+        <h1 style=font-size:25>{name}</h1>
+        <h1>Within the last week, <b>{num}</b> new entries for your subscribed rare diseases have been added to the {db_title} database</h1>
+        <table style="border:5 solid purple;margin:auto;text-align:center" width="750">
+        <tr>
+        <th>Name</th>
+        <th>GARD ID</th>
+        <th>Nodes Modified</th>
+        </tr>
+    """.format(num=data['total'],images_path=sysvars.images_path,db_title=txt_db[type],name=data['name'])
+
+    for gard in data['subscriptions']:
+        if data[gard]['num'] > 0:
+            full_msg += '{name} [{gardId}] - {num} new additions have been added to the database\n'.format(name=data[gard]['name'], num=data[gard]['num'], gardId=gard)
+            html += """
+                <tr>
+                <td><a href='https://rdas.ncats.nih.gov/disease?id={gardId}#{tab}'>{name}</a></td>
+                <td>{gardId}</td>
+                <td>{num}</td>
+                </tr>
+            """.format(name=data[gard]['name'], num=data[gard]['num'], gardId=gard, tab=tabs[type])
+
+    html += """
+        </table>
+        <h4>Results gathered within the time period of {date_start}-{date_end}</h4>
+        <br>
+        </div>
+        <div style="text-align:center">
+        <img src="https://upload.wikimedia.org/wikipedia/commons/6/6e/National_Center_for_Advancing_Translational_Sciences_logo.png" alt="Rare Disease Alert System" width="300" style="display:block;margin:auto">
+        <body>
+        <html>
+    """.format(date_start=data['update_date_start'],date_end=data['update_date_end'])
+
+    print(html)
+    return (full_msg,html)
+
+def send_mail(type, data):
+
+    print('type::',type)
+    print('data::',data)
+
+
+    # print(f"[{data['total']}, {data['email']}]")
+    # if data['total'] > 0 and data['email'] == '[email protected]' or data['email'] == '[email protected]':
+
+    #     # data['email'] = '[email protected]' # TEST EMAIL
+    #     data['email'] = '[email protected]' # TEST EMAIL
+    #     if type == "clinical":
+    #         txt,html = fill_template(type,data)
+    #         alert.send_email('RDAS-Alert: Clinical Trial update regarding your subscriptions', txt, data['email'], html=html) #data['email'] in place of email
+    #         print('[Email Sent...]')
+
+    #     if type == "pubmed":
+    #         txt,html = fill_template(type,data)
+    #         alert.send_email('RDAS-Alert: Publication update regarding your subscriptions', txt, data['email'], html=html)
+    #         print('[Email Sent...]')
+
+    #     if type == "grant":
+    #         txt,html = fill_template(type,data)
+    #         alert.send_email('RDAS-Alert: Funded Project update regarding your subscriptions', txt, data['email'], html=html)
+    #         print('[Email Sent...]')
+
+def get_stats(type, gards, date_start=datetime.today().strftime('%m/%d/%y'), date_end=datetime.today().strftime('%m/%d/%y')):
+    db = AlertCypher(type)
+    return_data = dict()
+
+    date_start_string = date_start
+    date_end_string = date_end
+    date_start_obj = datetime.strptime(date_start, '%m/%d/%y')
+    date_end_obj = datetime.strptime(date_end, '%m/%d/%y')
+
+    date_list = pd.date_range(date_start_obj, date_end_obj, freq='D').strftime('%m/%d/%y').to_list()
+
+    print(f'Searching for nodes created between {date_start_string} and {date_end_string}')
+
+    convert = {'clinical':['ClinicalTrial','GARD','GardId'], 'pubmed':['Article','GARD','GardId'], 'grant':['Project','GARD','GardId']}
+    connect_to_gard = {'clinical':'--(:Condition)--(:Annotation)--','pubmed':'--','grant':'--'}
+
+    query = 'MATCH (x:{node}){connection}(y:{gardnode}) WHERE x.DateCreatedRDAS IN {date_list} AND y.{property} IN {list} RETURN COUNT(x)'.format(node=convert[type][0], gardnode=convert[type][1], property=convert[type][2], list=list(gards.keys()), date_list=date_list, connection=connect_to_gard[type])
+
+    response = db.run(query)
+    return_data['total'] = response.data()[0]['COUNT(x)']
+
+    for gard in gards.keys():
+        response = db.run('MATCH (x:{node}){connection}(y:{gardnode}) WHERE x.DateCreatedRDAS IN {date_list} AND y.{property} = \"{gard}\" RETURN COUNT(x)'.format(node=convert[type][0], gardnode=convert[type][1], property=convert[type][2], gard=gard, date_list=date_list, connection=connect_to_gard[type]))
+        return_data[gard] = {'name':gards[gard],'num':response.data()[0]['COUNT(x)']}
+
+    return_data['update_date_end'] = date_end_string
+    return_data['update_date_start'] = date_start_string
+
+    return return_data
+
+def trigger_email(type,date_start=None,date_end=None):
+    convert = {'clinical':'trials', 'pubmed':'articles', 'grant':'grants'}
+    user_data = dict()
+    cred = credentials.Certificate(sysvars.firebase_key_path)
+    firebase_admin.initialize_app(cred)
+    firestore_db = firestore.client()
+
+    firestore_docs = firestore_db.collection(u'users').stream()
+
+    for doc in firestore_docs:
+        if doc.exists:
+            user_data[doc.id] = doc.to_dict()
+        else:
+            print('Document Doesnt Exist')
+
+    for firestore_user, data in user_data.items():
+        subscript_gard = dict()
+        for subscript in data['subscriptions']:
+            try:
+                if convert[type] in subscript['alerts']:
+                    subscript_gard[subscript['gardID']] = subscript['diseaseName']
+            except KeyError:
+                print('')
+                pass
+        users = auth.list_users()
+        if users:
+            users = users.iterate_all()
+            for user in users:
+                uid = user.uid
+                if uid == firestore_user and len(subscript_gard) > 0:
+                    if not date_start and not date_end:
+                        update_data = get_stats(type, subscript_gard)
+                    elif date_start and date_end:
+                        update_data = get_stats(type, subscript_gard, date_start=date_start, date_end=date_end)
+                    elif date_start:
+                        update_data = get_stats(type, subscript_gard, date_start=date_start)
+                    elif date_end:
+                        update_data = get_stats(type, subscript_gard, date_end=date_end)
+
+                    update_data['email'] = user.email
+                    update_data['name'] = user_data[uid]['displayName']
+                    update_data['subscriptions'] = list(subscript_gard.keys())
+                    send_mail(type, update_data)
+
+#trigger_email(sysvars.pm_db, date_start='12/07/22') #TEST