Production v1.4.0 [Email System Update]

.gitignore

@@ -43,4 +43,5 @@ migrated/*.dump
 approved/*.dump
 grant/raw/*
 grant/processed/*
+crt/*.json
 removethis.py

AlertCypher.py

@@ -17,7 +17,7 @@ def __init__(self, db):
         user = os.environ['NEO4J_USERNAME']
         password = os.environ['NEO4J_PASSWORD']
 
-        watch("neo4j")
+        #watch("neo4j")
 
         connection = GraphDatabase.driver(uri=server_uri, auth=(user, password)) #encrypted=True, trusted_certificates=TrustAll()
         self.session = connection.session(database=db)

crt/README.md

@@ -0,0 +1 @@
+# Location where the firebase access key will be stored

email/alert.py

@@ -1,83 +1,57 @@
-#import django
-#from django.core.mail import send_mail
-#from django.template.loader import render_to_string
-import os
 import boto3
 from botocore.exceptions import ClientError
-#os.environ['DJANGO_SETTINGS_MODULE'] = 'settings'
-#django.setup()
-'''
-def clinical_msg (data): # dict
-    msg_plain = render_to_string('templates/clinical_notif.txt', data)
-    msg_html = render_to_string('templates/clinical_notif.html', data)
 
-    send_mail(
-        'Test Email',
-        msg_plain,
-        'from-email <[email protected]>',
-        ['RECIPIENT'],
-        html_message=msg_html
-    )
-
-def pubmed_msg (data): # dict
-    msg_plain = render_to_string('templates/pubmed_notif.txt', data)
-    msg_html = render_to_string('templates/pubmed_notif.html', data)
+sender_email = '[email protected]'
 
-    send_mail(
-        'Test Email',
-        msg_plain,
-        'from-email <[email protected]>',
-        ['RECIPIENT'],
-        html_message=msg_html
+def setup_email_client():
+    client = boto3.client(
+        service_name='ses',
+        region_name='us-east-1'
     )
+    return client
 
-def grant_msg (data): # dict
-    msg_plain = render_to_string('templates/grant_notif.txt', data)
-    msg_html = render_to_string('templates/grant_notif.html', data)
-
-    send_mail(
-        'Test Email',
-        msg_plain,
-        'from-email <[email protected]>',
-        ['RECIPIENT'],
-        html_message=msg_html
-    )
+def send_email(sub,msg,recip,html=None,client=setup_email_client()):
+    if not client:
+        return
 
-def test_msg (sub, msg, recip):
-    send_mail(
-        f'{sub}',
-        f'{msg}',
-        '[email protected]',
-        [f'{recip}']
+    response = client.send_email(
+        Source=sender_email,
+        Destination={
+            'ToAddresses': [
+                f'{recip}',
+            ],
+        },
+        Message={
+            'Subject': {
+                'Data': f'{sub}',
+            },
+            'Body': {
+                'Text': {
+                    'Data': f'{msg}',
+                },
+                'Html': {
+                    'Data': f'{html}'
+                },
+            }
+        }
     )
-'''
-
-def get_secret():
 
-    secret_name = "/smtp/credentials"
-    region_name = "us-east-1"
+def send_raw_email(sub,msg,recip,client=None):
+    if not client:
+        return
 
-    # Create a Secrets Manager client
-    session = boto3.session.Session()
     client = session.client(
-        service_name='secretsmanager',
-        region_name=region_name
+        service_name='ses',
+        region_name='us-east-1'
+    )
+
+    response = client.send_raw_email(
+        Source='[email protected]',
+        Destinations=[
+            f'{recip}',
+        ],
+        RawMessage={
+            'Data': f'To:{recip}\nFrom:[email protected]\nSubject:{sub}\nMIME-Version: 1.0\nContent-type: Multipart/Mixed; boundary="NextPart"\n\n--NextPart\nContent-Type: text/plain\n\n{msg}\n\n'
+        },
     )
 
-    try:
-        get_secret_value_response = client.get_secret_value(
-            SecretId=secret_name
-        )
-    except ClientError as e:
-        # For a list of exceptions thrown, see
-        # https://docs.aws.amazon.com/secretsmanager/latest/apireference/API_GetSecretValue.html
-        raise e
-
-    # Decrypts secret using the associated KMS key.
-    secret = get_secret_value_response['SecretString']
-    print(secret)
-
-    # Your code goes here.
-
-get_secret()
-#test_msg('test','test','[email protected]')

email/ses_firebase.py

@@ -1,49 +1,107 @@
+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
 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:purple;'>
+        <div>
+        <img src="https://rdas.ncats.nih.gov/assets/rdas_final_gradient.png" alt="Rare Disease Alert System" style="display:block;margin:auto;">
+        </div>
+        <div style='text-align:center;background-color:white;padding:10px 100px 100px 100px;margin:10px 100px 100px 100px'>
+        <h1>{name}</h1>
+        <h1>On {date}, You have {num} new entries for your subscribed rare diseases in the {db_title} database</h1>
+        <h2>Out of that {num},</h2>
+        <br>
+        <p>
+    """.format(num=data['total'],images_path=sysvars.images_path,db_title=txt_db[type],name=data['name'],date=data['update_date'])
+
+    for gard in data['subscriptions']:
+        if data[gard]['num'] > 0:
+            full_msg += '{name} [{ID}] - {num} new additions have been added to the database\n'.format(name=data[gard]['name'], num=data[gard]['num'], ID=gard)
+            html += """
+                <a href='https://rdas.ncats.nih.gov/disease?id={ID}#{tab}'>{name} [{ID}]</a> - {num} new additions have been added to the database
+                <br>
+            """.format(name=data[gard]['name'], num=data[gard]['num'], ID=gard, tab=tabs[type])
+
+    html += """
+        <p>
+        </div>
+        <body>
+        <html>
+    """
+    return (full_msg,html)
 
 def send_mail(type, data):
-    if data['total'] > 0:
-
+    print(data['total'],data['email'])
+    if data['total'] > 0 and data['email'] == '[email protected]':
+
+        data['email'] = '[email protected]' # TEST EMAIL
+
         if type == "clinical":
-            print('To: {toemail}\nYou have {num} new entries for your subscribed rare diseases in the clinical trial database\nOut of that {num},\n'.format(toemail=data['email'],num=data['total']))
-            for gard in data['subscriptions']:
-                if data[gard]['num'] > 0:
-                    print('{name} [{ID}] - {num} new additions have been added to the database'.format(name=data[gard]['name'], num=data[gard]['num'], ID=gard))
-
-            #ses.clinical_msg() # pass in data for email as dict
-        elif type == "pubmed":
-            print('To: {toemail}\nYou have {num} new entries for your subscribed rare diseases'.format(toemail=data['email'],num=data['update_num']))
-            #ses.pubmed_msg()
-        elif type == "grant":
-            print('To: {toemail}\nYou have {num} new entries for your subscribed rare diseases'.format(toemail=data['email'],num=data['update_num']))
-            #ses.grant_msg()
-
-
-def get_stats(db, type, gards):
+            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=None):
+    db = AlertCypher(type)
     return_data = dict()
-    now = date.today()
-    now = now.strftime("%m/%d/%y")
-    #now = "12/27/22"
-    convert = {'clinical':['ClinicalTrial','GARD','GARDId'], 'pubmed':['Article','Disease','gard_id'], 'grant':['Project','Disease','gard_id']}
 
-    response = db.run('MATCH (x:{node})--(y:{gardnode}) WHERE x.DateCreated = \"{now}\" 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()), now=now))
+    if date:
+        now = date
+    else:
+        now = date.today()
+        now = now.strftime("%m/%d/%y")
+    print(f'Searching for nodes created on {now}')
+
+    convert = {'clinical':['ClinicalTrial','GARD','GardId'], 'pubmed':['Article','GARD','GardId'], 'grant':['Project','GARD','GardId']}
+    connect_to_gard = {'clinical':'--(:Condition)--(:Annotation)--','pubmed':'--','grant':'--'}
+
+    response = db.run('MATCH (x:{node}){connection}(y:{gardnode}) WHERE x.DateCreatedRDAS = \"{now}\" 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()), now=now, connection=connect_to_gard[type]))
     return_data['total'] = response.data()[0]['COUNT(x)']
 
     for gard in gards.keys():
-        response = db.run('MATCH (x:{node})--(y:{gardnode}) WHERE x.DateCreated = \"{now}\" AND y.{property} = \"{gard}\" RETURN COUNT(x)'
-            .format(node=convert[type][0], gardnode=convert[type][1], property=convert[type][2], gard=gard, now=now))
+        response = db.run('MATCH (x:{node}){connection}(y:{gardnode}) WHERE x.DateCreatedRDAS = \"{now}\" AND y.{property} = \"{gard}\" RETURN COUNT(x)'
+            .format(node=convert[type][0], gardnode=convert[type][1], property=convert[type][2], gard=gard, now=now, connection=connect_to_gard[type]))
         return_data[gard] = {'name':gards[gard],'num':response.data()[0]['COUNT(x)']}
 
+    return_data['update_date'] = now
     return return_data
 
-def trigger_email(db, type):
+def trigger_email(type,date=None):
     convert = {'clinical':'trials', 'pubmed':'articles', 'grant':'grants'}
     user_data = dict()
-    cred = credentials.Certificate('new\\firestore\\key.json')
+    cred = credentials.Certificate(sysvars.firebase_key_path)
     firebase_admin.initialize_app(cred)
     firestore_db = firestore.client()
 
@@ -55,23 +113,25 @@ def trigger_email(db, type):
         else:
             print(u'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:
-                    update_data = get_stats(db, type, subscript_gard)
+                if uid == firestore_user and len(subscript_gard) > 0:
+                    update_data = get_stats(type, subscript_gard, date)
                     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.gnt_db, '04/27/23')