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Minghui dev #55

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Minghui dev #55

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12d44bc
test pull
MingghuiA Feb 13, 2024
2b5753d
Minghui development (#50)
MingghuiA Feb 14, 2024
f3f5ae8
update start_dev.py and email alert model to combine the three databa…
MingghuiA May 23, 2024
c9b5922
remove unused file
MingghuiA May 23, 2024
3c2052d
add codes to manage all database names on sysvars.py
MingghuiA May 24, 2024
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16 changes: 12 additions & 4 deletions config.ini
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Original file line number Diff line number Diff line change
Expand Up @@ -12,10 +12,18 @@ pm_interval = 7
gnt_interval = 365
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
; minghui.clinical_update = 01/08/24
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confused on what these lines are with the ; symbol

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@MingghuiA MingghuiA May 24, 2024 •
edited
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the ; symbol means these lines are commented out

; minghui.grant_update = 11/30/22
; minghui.pubmed_update = 10/30/22
; minghui.gard_update = 11/30/23
; minghui.rdas.ctkg_update = 05/15/24
; minghui.rdas.gfkg_update = 05/01/24
; minghui.rdas.pakg_update = 05/15/24
; minghui.rdas.gard_update = 05/15/24
minghui.rdas.ctkg_update = 01/01/24
minghui.rdas.gfkg_update = 01/01/23
minghui.rdas.pakg_update = 01/01/24
minghui.rdas.gard_update = 01/01/24

[TEST_TRANSFER_DETECTION]
clinical =
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164 changes: 0 additions & 164 deletions email/ses_firebase.py
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58 changes: 42 additions & 16 deletions emails/alert.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,7 @@
import boto3
import sys
sys.path.append('/home/aom2/RDAS')
sys.path.append('/home/aom2/RDAS/emails')
from botocore.exceptions import ClientError

sender_email = 'ncatsrdas@mail.nih.gov'
Expand All @@ -10,31 +13,54 @@ def setup_email_client():
)
return client

def send_email(sub,msg,recip,html=None,client=setup_email_client()):
if not client:
return

response = client.send_email(
Source=sender_email,
Destination={
'ToAddresses': [
f'{recip}',
],
},
Message={
def send_email(subject, html, recipient, client=setup_email_client()):
print("Sending emails to:", recipient)
# sender_email = client # Replace with your email
# Set up the email
message={
'Subject': {
'Data': f'{sub}',
'Data': f'{subject}',
},
'Body': {
'Text': {
'Data': f'{msg}',
},

'Html': {
'Data': f'{html}'
},
}
}


# Send the email
response = client.send_email(
Source=sender_email,
Destination={'ToAddresses': [recipient]},
Message=message
)
print("Email sent successfully.")


# def send_email(sub,html,recip,client=setup_email_client()):
# if not client:
# return

# response = client.send_email(
# Source=sender_email,
# Destination={
# 'ToAddresses': [
# f'{recip}',
# ],
# },
# Message={
# 'Subject': {
# 'Data': f'{sub}',
# },
# 'Body': {
# 'Html': {
# 'Data': f'{html}'
# },
# }
# }
# )

def send_raw_email(sub,msg,recip,client=None):
if not client:
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32 changes: 0 additions & 32 deletions emails/email_template1.html
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84 changes: 84 additions & 0 deletions emails/email_template3.html
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Original file line number Diff line number Diff line change
@@ -0,0 +1,84 @@
<!-- 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:50px; color:purple;">Rare Disease Alert System</h1>
<h2>{{ data['name'] }}</h2>
<h3>You have {{ data['total'] }} new entries for your subscribed rare diseases in the database</h3>
<table border="1" style="margin: auto;">
<tr>
<th>Name</th>
<th>GARD ID</th>
<th>New Articles Number</th>
<th>New Clinical Trials Number</th>
<th>New Funding Project Number</th>
</tr>
{% for gard_id, gard_name in data['subscriptions'].items() %}
{% set articles = data[gard_id].get('articles', 0) %}
{% set trials = data[gard_id].get('trials', 0) %}
{% set grants = data[gard_id].get('grants', 0) %}
{% if articles > 0 or trials > 0 or grants > 0 %}
<tr>
<td><a href="https://rdas.ncats.nih.gov/disease?id={{ gard_id }}"> {{ gard_name }} </a></td>
<td>{{ gard_id }}</td>
<td>{{ articles }}</td>
<td>{{ trials }}</td>
<td>{{ grants }}</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> -->

<body style="text-align: center;">
<h1 style="font-size:50px; color:purple;">Rare Disease Alert System</h1>
<!-- <h2>{{ data['name'] }}</h2> -->
<h3>You have {{ data['total'] }} new entries for your subscribed rare diseases in the database</h3>
<table border="1" style="margin: auto;">
<tr>
<th>Disease Name</th>
<th>GARD ID</th>
{% for dataset in data['datasets'] %}
{% if dataset == 'articles' %}
<th>New Articles</th>
{% elif dataset == 'trials' %}
<th>New Clinical Trials</th>
{% elif dataset == 'grants' %}
<th>New Fundings</th>
{% endif %}
{% endfor %}
</tr>
{% for gard_id, gard_name in data['subscriptions'].items() %}
{% set articles = data[gard_id].get('articles', 0) %}
{% set trials = data[gard_id].get('trials', 0) %}
{% set grants = data[gard_id].get('grants', 0) %}
{% if articles > 0 or trials > 0 or grants > 0 %}
<tr>
<td><a href="https://rdas.ncats.nih.gov/disease?id={{ gard_id }}"> {{ gard_name }} </a></td>
<td>{{ gard_id }}</td>
{% for dataset in data['datasets'] %}
{% if dataset == 'articles' %}
<td>{{ articles }}</td>
{% elif dataset == 'trials' %}
<td>{{ trials }}</td>
{% elif dataset == 'grants' %}
<td>{{ grants }}</td>
{% endif %}
{% endfor %}
</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>
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