Merge pull request #17 from bioimage-io/forward_emails

Emails!

.github/workflows/emails_to_chat.yaml

@@ -0,0 +1,27 @@
+name: forward emails to chat
+
+on:
+  schedule:
+    - cron: "0 * * * *" # every hour at minute 0
+
+concurrency: forward-emails-to-chat
+
+env:
+  S3_HOST: ${{vars.S3_HOST}}
+  S3_BUCKET: ${{vars.S3_BUCKET}}
+  S3_FOLDER: ${{vars.S3_FOLDER}}
+  S3_ACCESS_KEY_ID: ${{secrets.S3_ACCESS_KEY_ID}}
+  S3_SECRET_ACCESS_KEY: ${{secrets.S3_SECRET_ACCESS_KEY}}
+  MAIL_PASSWORD: ${{secrets.MAIL_PASSWORD}}
+
+jobs:
+  run:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: "pip" # caching pip dependencies
+      - run: pip install .
+      - run: backoffice forward-emails-to-chat

.github/workflows/publish_call.yaml

@@ -46,8 +46,3 @@ jobs:
           cache: "pip" # caching pip dependencies
       - run: pip install .
       - run: backoffice publish "${{ inputs.resource_id }}" "staged/${{ inputs.stage_number }}"
-      # - name: Publish to Zenodo
-      #   run: |
-      #     python .github/scripts/update_status.py "${{ inputs.resource_path }}" "Publishing to Zenodo" "5"
-      #     python .github/scripts/upload_model_to_zenodo.py --resource_path "${{inputs.resource_path}}"
-      #     python .github/scripts/update_status.py "${{ inputs.resource_path }}" "Publishing complete" "6"

backoffice/_backoffice.py

@@ -9,6 +9,7 @@
 from backoffice.backup import backup
 from backoffice.generate_collection_json import generate_collection_json
 from backoffice.gh_utils import set_gh_actions_outputs
+from backoffice.mailroom import forward_emails_to_chat, notify_uploader
 from backoffice.remote_resource import (
     PublishedVersion,
     RemoteResource,
@@ -90,6 +91,12 @@ def await_review(self, resource_id: str, version: str):
                 f"Cannot await review for already published {resource_id} {version}"
             )
         rv.await_review()
+        notify_uploader(
+            rv,
+            "is awaiting review ⌛",
+            f"Thank you for proposing {rv.id} {rv.version}!\n"
+            + "Our maintainers will take a look shortly!",
+        )
 
     def request_changes(self, resource_id: str, version: str, reason: str):
         """mark a (staged) resource version as needing changes"""
@@ -100,6 +107,13 @@ def request_changes(self, resource_id: str, version: str, reason: str):
             )
 
         rv.request_changes(reason=reason)
+        notify_uploader(
+            rv,
+            "needs changes 📑",
+            f"Thank you for proposing {rv.id} {rv.version}!\n"
+            + "We kindly ask you to upload an updated version, because: \n"
+            + f"{reason}\n",
+        )
 
     def publish(self, resource_id: str, version: str):
         """publish a (staged) resource version"""
@@ -111,6 +125,13 @@ def publish(self, resource_id: str, version: str):
 
         published: PublishedVersion = rv.publish()
         assert isinstance(published, PublishedVersion)
+        self.generate_collection_json()
+        notify_uploader(
+            rv,
+            "was published! 🎉",
+            f"Thank you for contributing {published.id} {published.version} to bioimage.io!\n"
+            + "Check it out at https://bioimage.io/#/?id={published.id}\n",  # TODO: link to version
+        )
 
     def backup(self, destination: Optional[str] = None):
         """backup the whole collection (to zenodo.org)"""
@@ -121,3 +142,6 @@ def generate_collection_json(
     ):
         """generate the collection.json file --- a summary of the whole collection"""
         generate_collection_json(self.client, collection_template=collection_template)
+
+    def forward_emails_to_chat(self):
+        forward_emails_to_chat(self.client, last_n_days=7)

backoffice/mailroom/__init__.py

@@ -0,0 +1,3 @@
+from ._forward_emails_to_chat import forward_emails_to_chat as forward_emails_to_chat
+from ._send_email import notify_uploader as notify_uploader
+from ._send_email import send_email as send_email

backoffice/mailroom/_forward_emails_to_chat.py

@@ -0,0 +1,162 @@
+import email.message
+import email.parser
+import imaplib
+import os
+from contextlib import contextmanager
+from datetime import datetime, timedelta
+from email.utils import parsedate_to_datetime
+from typing import Any
+
+from dotenv import load_dotenv
+from loguru import logger
+
+from backoffice.mailroom.constants import (
+    BOT_EMAIL,
+    IMAP_PORT,
+    REPLY_HINT,
+    SMTP_SERVER,
+    STATUS_UPDATE_SUBJECT,
+)
+from backoffice.remote_resource import get_remote_resource_version
+from backoffice.s3_client import Client
+from backoffice.s3_structure.chat import Chat, Message
+
+_ = load_dotenv()
+
+
+FORWARDED_TO_CHAT_FLAT = "forwarded-to-bioimageio-chat"
+
+
+def forward_emails_to_chat(s3_client: Client, last_n_days: int):
+    cutoff_datetime = datetime.now().astimezone() - timedelta(days=last_n_days)
+    with _get_imap_client() as imap_client:
+        _update_chats(s3_client, imap_client, cutoff_datetime)
+
+
+@contextmanager
+def _get_imap_client():
+    imap_client = imaplib.IMAP4_SSL(SMTP_SERVER, IMAP_PORT)
+    _ = imap_client.login(BOT_EMAIL, os.environ["MAIL_PASSWORD"])
+    yield imap_client
+    _ = imap_client.logout()
+
+
+def _get_body(msg: email.message.Message):
+    if msg.is_multipart():
+        for part in msg.walk():
+            ctype = part.get_content_type()
+            cdispo = str(part.get("Content-Disposition"))
+
+            # skip any text/plain (txt) attachments
+            if ctype == "text/plain" and "attachment" not in cdispo:
+                msg_part = part
+                break
+        else:
+            logger.error("faild to get body from multipart message: {}", msg)
+            return None
+    else:
+        # not multipart - i.e. plain text, no attachments, keeping fingers crossed
+        msg_part = msg
+
+    msg_bytes = msg_part.get_payload(decode=True)
+    try:
+        body = str(msg_bytes, "utf-8")  # pyright: ignore[reportArgumentType]
+    except Exception as e:
+        logger.error("failed to decode email body: {}", e)
+        return None
+    else:
+        return body
+
+
+def _update_chats(
+    s3_client: Client, imap_client: imaplib.IMAP4_SSL, cutoff_datetime: datetime
+):
+    _ = imap_client.select("inbox")
+    for msg_id, rid, rv, msg, dt in _iterate_relevant_emails(
+        imap_client, cutoff_datetime
+    ):
+        ok, flag_data = imap_client.fetch(str(msg_id), "(FLAGS)")
+        if ok != "OK" or len(flag_data) != 1:
+            logger.error("failed to get flags for {}", msg_id)
+            continue
+        try:
+            assert isinstance(flag_data[0], bytes), type(flag_data[0])
+            flags = str(flag_data[0], "utf-8")
+        except Exception as e:
+            logger.error("failed to interprete flags '{}': {}", flag_data[0], e)
+            continue
+
+        if FORWARDED_TO_CHAT_FLAT in flags:
+            continue  # already processed
+
+        body = _get_body(msg)
+        if body is None:
+            continue
+
+        sender = msg["from"]
+        text = "[forwarded from email]\n" + body.replace("> " + REPLY_HINT, "").replace(
+            REPLY_HINT, ""
+        )
+        rr = get_remote_resource_version(s3_client, rid, rv)
+        if not rr.exists():
+            logger.error("Cannot comment on non-existing resource {} {}", rid, rv)
+            continue
+
+        rr.extend_chat(Chat(messages=[Message(author=sender, text=text, timestamp=dt)]))
+        _ = imap_client.store(str(msg_id), "+FLAGS", FORWARDED_TO_CHAT_FLAT)
+
+
+def _iterate_relevant_emails(imap_client: imaplib.IMAP4_SSL, cutoff_datetime: datetime):
+    for msg_id, msg, dt in _iterate_emails(imap_client, cutoff_datetime):
+        subject = str(msg["subject"])
+        if STATUS_UPDATE_SUBJECT not in subject:
+            logger.debug("ignoring subject: '{}'", subject)
+            continue
+
+        try:
+            _, id_version = subject.split(STATUS_UPDATE_SUBJECT)
+            resource_id, resource_version = id_version.strip().split(" ")
+        except Exception:
+            logger.warning("failed to process subject: {}", subject)
+            continue
+
+        yield msg_id, resource_id, resource_version, msg, dt
+
+
+def _iterate_emails(imap_client: imaplib.IMAP4_SSL, cutoff_datetime: datetime):
+    data = imap_client.search(None, "ALL")
+    mail_ids = data[1]
+    id_list = mail_ids[0].split()
+    first_email_id = int(id_list[0])
+    latest_email_id = int(id_list[-1])
+
+    for msg_id in range(latest_email_id, first_email_id, -1):
+        ok, msg_data = imap_client.fetch(str(msg_id), "(RFC822)")
+        if ok != "OK":
+            logger.error("failed to fetch email {}", msg_id)
+            continue
+
+        parts = [p for p in msg_data if isinstance(p, tuple)]
+        if len(parts) == 0:
+            logger.error("found email with without any parts")
+            continue
+        elif len(parts) > 1:
+            logger.error(
+                "found email with multiple parts. I'll only look at the first part"
+            )
+
+        _, msg_part = parts[0]
+
+        msg = email.message_from_string(str(msg_part, "utf-8"))
+        dt: Any = parsedate_to_datetime(msg["date"])
+        if isinstance(dt, datetime):
+            if dt < cutoff_datetime:
+                break
+        else:
+            logger.error("failed to parse email datetime '{}'", msg["date"])
+
+        yield msg_id, msg, dt
+
+
+if __name__ == "__main__":
+    forward_emails_to_chat(Client(), 7)

backoffice/mailroom/_send_email.py

@@ -0,0 +1,57 @@
+import os
+import smtplib
+from email.mime.text import MIMEText
+
+from dotenv import load_dotenv
+from loguru import logger
+
+from backoffice.mailroom.constants import (
+    BOT_EMAIL,
+    REPLY_HINT,
+    SMTP_PORT,
+    SMTP_SERVER,
+    STATUS_UPDATE_SUBJECT,
+)
+from backoffice.remote_resource import PublishedVersion, StagedVersion
+
+_ = load_dotenv()
+
+
+def notify_uploader(rv: StagedVersion | PublishedVersion, subject_end: str, msg: str):
+    email, name = rv.get_uploader()
+    if email is None:
+        logger.error("missing uploader email for {} {}", rv.id, rv.version)
+    else:
+        send_email(
+            subject=f"{STATUS_UPDATE_SUBJECT}{rv.id} {rv.version} {subject_end.strip()}",
+            body=(
+                f"Dear {name},\n"
+                + f"{msg.strip()}\n"
+                + "Kind regards,\n"
+                + "The bioimage.io bot 🦒\n"
+                + REPLY_HINT
+            ),
+            recipients=[email],
+        )
+
+
+def send_email(subject: str, body: str, recipients: list[str]):
+    from_addr = BOT_EMAIL
+    to_addr = ", ".join(recipients)
+    msg = MIMEText(body)
+    msg["From"] = from_addr
+    msg["To"] = to_addr
+    msg["Subject"] = subject
+    with smtplib.SMTP_SSL(SMTP_SERVER, SMTP_PORT) as smtp_server:
+        _ = smtp_server.login(BOT_EMAIL, os.environ["MAIL_PASSWORD"])
+        _ = smtp_server.sendmail(BOT_EMAIL, recipients, msg.as_string())
+
+    logger.info("Email '{}' sent to {}", subject, recipients)
+
+
+if __name__ == "__main__":
+    send_email(
+        subject=STATUS_UPDATE_SUBJECT + " lazy-bug staged/2",
+        body="Staged version 2 of your model 'lazy-bug' is now under review.",
+        recipients=["[email protected]"],
+    )