Merge pull request #48 from CCBR/email

feat: send the report via email and push to github

bin/render_report_biowulf.sh

@@ -3,7 +3,22 @@
 # Usage: bash bin/render_report_biowulf.sh
 module load singularity
 SINGULARITY_CACHEDIR=/data/CCBR_Pipeliner/SIFS
-echo "cd /mnt && Rscript bin/render.R" |\
-    singularity exec -C -B $PWD:/mnt,/data/CCBR_Pipeliner/userdata/spacesavers2/:/mnt/data docker://nciccbr/spacesavers2:0.1.1 bash
+
 today=$(date +'%Y-%m-%d')
-cp docs/report.html docs/report_${today}.html
+year=$(date +'%Y')
+mkdir -p docs/$year
+html_filename="docs/${year}/report_${today}.html"
+recipient_email="kelly.sovacool@nih.gov"
+
+echo "cd /mnt && \
+    Rscript bin/render.R && \
+    cp docs/report.html $html_filename && \
+    python src/send_email.py \
+        $html_filename \
+        $recipient_email \
+    " |\
+    singularity exec -C -B $PWD:/mnt,/data/CCBR_Pipeliner/userdata/spacesavers2/:/mnt/data docker://nciccbr/spacesavers2:0.1.1 bash
+
+git add docs
+git commit -m 'chore: render report 🤖'
+git push

report.Rmd

@@ -19,6 +19,8 @@ knit: (function(inputFile, encoding) {
 knitr::opts_chunk$set(message = FALSE, warning = FALSE)
 ```
 
+View this report on the web: `r glue::glue("<https://ccbr.github.io/spacesavers2/{lubridate::year(lubridate::today())}/report_{lubridate::today()}.html>")`
+
 ```{r load}
 library(bslib)
 library(dplyr)

src/send_email.py

@@ -0,0 +1,54 @@
+#!/usr/bin/env python
+
+""" Email the html report
+
+Usage:
+    python src/send_email.py <report_html> <recipient_emails>
+
+Example:
+    python src/send_email.py docs/report.html kelly.sovacool@nih.gov
+    python src/send_email.py docs/2024/report_2024-01-17.html kelly.sovacool@nih.gov,vishal.koparde@nih.gov
+
+"""
+
+import datetime
+from email.message import EmailMessage
+import os
+import smtplib
+import sys
+
+
+def send_email(
+    subject="test email from python",
+    plain_text=None,
+    html_attach = None,
+    sender="kelly.sovacool@nih.gov",
+    recipient="kelly.sovacool@nih.gov"
+):
+    msg = EmailMessage()
+    msg["Subject"] = subject
+    msg["From"] = sender
+    msg["To"] = recipient
+
+    if plain_text:
+        msg.set_content(plain_text)
+    if html_attach:
+        with open(html_attach, 'rb') as file:
+            html_data = file.read()
+        msg.add_attachment(html_data, 
+                           filename = os.path.basename(html_attach),
+                           maintype = 'text', subtype = 'html')
+
+    with smtplib.SMTP("localhost") as server:
+        server.send_message(msg)
+
+
+if __name__ == "__main__":
+    html_filename = sys.argv[1] if len(sys.argv) > 1 else ''
+    recipient_addr = sys.argv[2] if len(sys.argv) > 2 else 'kelly.sovacool@nih.gov'
+    send_email(
+        subject=f"🚀 spacesavers2 report",
+        recipient=recipient_addr,
+        plain_text = f"Download the attached report or view it at https://ccbr.github.io/spacesavers2/{html_filename.strip('docs/')}\n\nThis is an automated email.",
+        html_attach = html_filename
+    )