finish mail

.dockerignore

@@ -0,0 +1,19 @@
+.git/
+.github/
+.dockerignore
+Dockerfile
+
+*~
+*.DS_Store
+*.egg-info/
+__pycache__/
+
+.docker
+
+.idea/
+.vscode/
+
+examples/
+
+venv/
+/__

.gitignore

@@ -1 +1,13 @@
 /__
+
+*~
+*.DS_Store
+*.egg-info/
+__pycache__/
+
+.docker
+
+.idea/
+.vscode/
+
+venv/

Dockerfile

@@ -0,0 +1,17 @@
+# Python version can be changed, e.g.
+FROM docker.io/python:3.11.3-slim-bullseye
+
+LABEL org.opencontainers.image.authors="FNNDSC <[email protected]>" \
+      org.opencontainers.image.title="An email plugin" \
+      org.opencontainers.image.description="A ChRIS plugin for email"
+
+ARG SRCDIR=/usr/local/src/mail
+RUN mkdir -p ${SRCDIR}
+WORKDIR ${SRCDIR}
+
+COPY . .
+RUN pip install "." \
+    && cd / && rm -rf ${SRCDIR}
+WORKDIR /
+
+CMD ["mail"]

README.md

@@ -1,2 +1,3 @@
-pl_mail
-==========
+# pl_mail
+
+A ChRIS Plugin for sending email.

mail.py

@@ -0,0 +1,94 @@
+#!/usr/bin/env python
+
+from pathlib import Path
+from argparse import ArgumentParser, Namespace
+
+import os
+import os.path
+
+import smtplib
+from email.message import EmailMessage
+
+from chris_plugin import chris_plugin
+from pflog import pflog
+
+
+parser = ArgumentParser(description='A ChRIS plugin to send email')
+parser.add_argument('-r', '--rcpt', type=str, required=False, default='', help='comma separated receipients. [inputdir]/rcpt if not specified in argument.')
+parser.add_argument('-t', '--title', type=str, required=False, default='', help='email title. [inputdir]/title if not specified in argument.')
+parser.add_argument('-c', '--content', type=str, required=False, default='', help='content. [inputdir]/content if not specified in argument.')
+
+parser.add_argument('-s', '--sender', type=str, required=False, default='[email protected]', help='sender (from). use [inputdir]/sender if exists.')
+parser.add_argument('-m', '--mailserver', type=str, required=False, default='postfix.postfix.svc.k8s.galena.fnndsc', help='email server. use [inputdir]/mailserver if exists.')
+
+
+@chris_plugin(
+    parser=parser,
+    title='A ChRIS plugin to send email',
+    category='',  # ref. https://chrisstore.co/plugins
+    min_memory_limit='500Mi',  # supported units: Mi, Gi
+    min_cpu_limit='1000m',  # millicores, e.g. "1000m" = 1 CPU core
+    min_gpu_limit=0,  # set min_gpu_limit=1 to enable GPU
+)
+@pflog.tel_logTime(
+    event       = 'email',
+    log         = 'Email',
+)
+def main(options: Namespace, inputdir: Path, outputdir: Path):
+    filename = os.sep.join([inputdir, 'rcpt'])
+    rcpt = _args_or_filename(options.rcpt, filename, 'Email: no --rcpt and no [inputdir]/rcpt')
+
+    filename = os.sep.join([inputdir, 'title'])
+    title = _args_or_filename(options.title, filename, 'Email: no --title and no [inputdir]/title')
+
+    filename = os.sep.join([inputdir, 'content'])
+    content = _args_or_filename(options.content, filename, 'Email: no --content and no [inputdir]/content')
+
+    filename = os.sep.join([inputdir, 'sender'])
+    sender = _filename_or_args(options.sender, filename, 'Email: no --sender and no [inputdir]/sender')
+
+    filename = os.sep.join([inputdir, 'mailserver'])
+    mail_server = _filename_or_args(options.mailserver, filename, 'Email: no --mailserver and no [inputdir]/mailserver')
+
+    _send_email(title=title, content=content, recipients=rcpt, mail_server=mail_server, sender=sender)
+
+
+def _args_or_filename(arg, filename, err_msg):
+    if arg:
+        return arg
+
+    if not os.path.exists(filename):
+        raise RuntimeError(err_msg)
+
+    with open(filename, 'r') as f:
+        return f.read().strip()
+
+
+def _filename_or_args(filename, arg, err_msg):
+    if os.path.exists(filename):
+        with open(filename, 'r') as f:
+            return f.read().strip()
+
+    if arg:
+        return arg
+
+    raise RuntimeError(err_msg)
+
+
+def _send_email(title, content, recipients, mail_server, sender):
+    if not recipients:
+        raise RuntimeError('Email: no --rcpt and no [inputdir]/rcpt')
+
+    msg = EmailMessage()
+    msg['Subject'] = title
+    msg['From'] = sender
+    msg['To'] = recipients
+    msg.set_content(content)
+
+    s = smtplib.SMTP(mail_server)
+    s.send_message(msg)
+    s.quit()
+
+
+if __name__ == '__main__':
+    main()

setup.py

@@ -6,17 +6,29 @@
 setuptools.setup(
     name='pl-mail',
     version='0.0.1',
-    author='',
-    author_email='',
-    description='',
+    author='FNNDSC',
+    author_email='[email protected]',
+    description='A ChRIS plugin for email',
     long_description=long_description,
     long_description_content_type='text/markdown',
     url='',
-    packages=setuptools.find_packages(exclude=['test*']),
+    py_modules=['mail'],
+    license='MIT',
+    entry_points={
+        'console_scripts': [
+            'mail = mail:main',
+        ]
+    },
     install_requires=[
+        'chris_plugin',
+        'pflog',
     ],
     classifiers=[
+        'License :: OSI Approved :: MIT License',
         'Programming Language :: Python :: 3',
         'Operating System :: OS Independent',
-    ],
+        'Topic :: Scientific/Engineering',
+        'Topic :: Scientific/Engineering :: Bio-Informatics',
+        'Topic :: Scientific/Engineering :: Medical Science Apps.'
+   ],
 )