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Production v1.4.0 [Email System Update]
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@@ -43,4 +43,5 @@ migrated/*.dump | |
approved/*.dump | ||
grant/raw/* | ||
grant/processed/* | ||
crt/*.json | ||
removethis.py |
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# Location where the firebase access key will be stored |
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@@ -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]' | ||
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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 | ||
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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}' | ||
}, | ||
} | ||
} | ||
) | ||
''' | ||
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def get_secret(): | ||
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secret_name = "/smtp/credentials" | ||
region_name = "us-east-1" | ||
def send_raw_email(sub,msg,recip,client=None): | ||
if not client: | ||
return | ||
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# 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' | ||
) | ||
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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' | ||
}, | ||
) | ||
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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 | ||
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# Decrypts secret using the associated KMS key. | ||
secret = get_secret_value_response['SecretString'] | ||
print(secret) | ||
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# Your code goes here. | ||
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get_secret() | ||
#test_msg('test','test','[email protected]') |
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@@ -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 = '' | ||
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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]) | ||
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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']) | ||
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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]) | ||
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html += """ | ||
<p> | ||
</div> | ||
<body> | ||
<html> | ||
""" | ||
return (full_msg,html) | ||
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def send_mail(type, data): | ||
if data['total'] > 0: | ||
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print(data['total'],data['email']) | ||
if data['total'] > 0 and data['email'] == '[email protected]': | ||
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data['email'] = '[email protected]' # TEST EMAIL | ||
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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)) | ||
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#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() | ||
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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...') | ||
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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...') | ||
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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...') | ||
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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']} | ||
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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}') | ||
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convert = {'clinical':['ClinicalTrial','GARD','GardId'], 'pubmed':['Article','GARD','GardId'], 'grant':['Project','GARD','GardId']} | ||
connect_to_gard = {'clinical':'--(:Condition)--(:Annotation)--','pubmed':'--','grant':'--'} | ||
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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)'] | ||
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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)']} | ||
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return_data['update_date'] = now | ||
return return_data | ||
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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() | ||
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@@ -55,23 +113,25 @@ def trigger_email(db, type): | |
else: | ||
print(u'Document Doesnt Exist') | ||
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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 | ||
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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) | ||
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trigger_email(sysvars.gnt_db, '04/27/23') |
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