From a1b44fd47d49086bbe0750dc19599040f878a965 Mon Sep 17 00:00:00 2001
From: Jim Klo <jimklo@stanford.edu>
Date: Tue, 16 Jun 2026 23:31:27 +0000
Subject: [PATCH 1/2] updates to make miqa phase 1 to build in 2026 and run in
 CB cluster.

---
 devops/docker/Dockerfile         | 48 ++++++++++++++++++++++++--------
 devops/docker/docker-compose.yml |  5 ++--
 devops/docker/entrypoint.sh      | 16 ++++++++---
 devops/docker/provision.yml      |  2 ++
 server/miqa_server/__init__.py   | 37 ++++++++++++++++++++++++
 server/miqa_server/email.py      |  8 +++++-
 server/setup.py                  |  1 +
 7 files changed, 98 insertions(+), 19 deletions(-)

diff --git a/devops/docker/Dockerfile b/devops/docker/Dockerfile
index 30f706d..4b8cffb 100644
--- a/devops/docker/Dockerfile
+++ b/devops/docker/Dockerfile
@@ -1,14 +1,29 @@
-FROM node:10.24.0-buster
+FROM node:10.24.1-buster
 
 EXPOSE 8080
 
-RUN apt-get update && apt-get install -qy \
+# Debian 10/Buster is archived now.
+RUN set -eux; \
+  printf '%s\n' \
+    'deb http://archive.debian.org/debian buster main contrib non-free' \
+    'deb http://archive.debian.org/debian-security buster/updates main contrib non-free' \
+    'deb http://archive.debian.org/debian buster-updates main contrib non-free' \
+    > /etc/apt/sources.list; \
+  printf 'Acquire::Check-Valid-Until "false";\n' > /etc/apt/apt.conf.d/99archive; \
+  apt-get update; \
+  apt-get install -qy --no-install-recommends \
+    build-essential \
     gcc \
+    git \
+    libffi-dev \
     libpython3-dev \
+    libsasl2-dev \
+    python3-dev \
     python3-pip \
-    git \
-    libsasl2-dev && \
-  apt-get clean && rm -rf /var/lib/apt/lists/*
+    python3-setuptools \
+    python3-wheel; \
+  apt-get clean; \
+  rm -rf /var/lib/apt/lists/*
 
 # See http://click.pocoo.org/5/python3/#python-3-surrogate-handling for more detail on
 # why this is necessary.
@@ -25,25 +40,36 @@ api_root = \"${GIRDER_API_ROOT}\"\n\
 static_public_path = \"${GIRDER_STATIC_PUBLIC_PATH}\"\n"\
 >> /etc/girder.cfg
 
+# patch install
+RUN python3 -m pip install --no-cache-dir --upgrade "pip<24" "setuptools<60" wheel
+RUN python3 -m pip install --no-cache-dir \
+    setuptools_scm==7.1.0 \
+    bcrypt==3.1.0 \
+    "pymongo>=3.6,<4"
+
 # Install girder
 RUN mkdir /miqa
 COPY server/ /miqa/server/
-RUN pip3 install /miqa/server
+RUN python3 -m pip install --no-cache-dir /miqa/server
 RUN girder build
 
 # Install miqa
 COPY client /miqa/client
 WORKDIR /miqa/client
-RUN npm install \
-    && npm run build \
+RUN npm ci --no-audit --no-fund --verbose \
+    && npm run build --verbose \
     && mv dist /usr/share/girder/static/miqa
 
 # Add sample data
 COPY sample_data /miqa/sample_data
 RUN sed -i 's/~//g' /miqa/sample_data/sample.json
 
-RUN git clone https://github.com/girder/girder.git girder_repo \
-    && pip3 install ansible \
+RUN git init girder_repo \
+    && cd girder_repo \
+    && git remote add origin https://github.com/girder/girder.git \
+    && git fetch --depth 1 origin ceb7074aa20582c3716ea322cfd5755bf37f0cfb \
+    && git checkout FETCH_HEAD \
+    && python3 -m pip install --no-cache-dir "ansible~=2.7" \
     && ansible-galaxy install -p /girder_repo/devops/ansible/roles girder.girder
 RUN pip3 install girder_client
 COPY devops/docker/provision.yml /provision.yml
@@ -51,4 +77,4 @@ COPY devops/docker/inventory /etc/ansible/hosts
 ENV ANSIBLE_LIBRARY=/girder_repo/devops/ansible/roles/girder.girder/library
 
 COPY devops/docker/entrypoint.sh /entrypoint.sh
-ENTRYPOINT ["bash", "/entrypoint.sh"]
\ No newline at end of file
+ENTRYPOINT ["bash", "/entrypoint.sh"]
diff --git a/devops/docker/docker-compose.yml b/devops/docker/docker-compose.yml
index a452302..565a1d9 100644
--- a/devops/docker/docker-compose.yml
+++ b/devops/docker/docker-compose.yml
@@ -1,4 +1,3 @@
-version: "2"
 
 services:
   database:
@@ -25,11 +24,11 @@ services:
     command:
       [
         "database:27017",
-        "admin_name=${GIRDER_ADMIN_NAME} admin_pass=${GIRDER_ADMIN_PASS} admin_email=${GIRDER_ADMIN_USER_EMAIL} smtp_server=${GIRDER_SMTP_RELAY} smtp_port=${GIRDER_SMTP_PORT} smtp_encryption=${GIRDER_SMTP_CRYPTO} smtp_username=${GIRDER_SMTP_USER} smtp_password=${GIRDER_SMTP_PASSWD} server_url_in_email=${SERVER_URL_IN_EMAIL} sender_address=${SENDER_ADDRESS} sample_data=${SAMPLE_DATA} session_timeout=${MIQA_SESSION_TIMEOUT}",
+        "admin_name=${GIRDER_ADMIN_NAME} admin_pass=${GIRDER_ADMIN_PASS} admin_email=${GIRDER_ADMIN_USER_EMAIL} smtp_server=${GIRDER_SMTP_RELAY} smtp_port=${GIRDER_SMTP_PORT} smtp_encryption=${GIRDER_SMTP_CRYPTO} smtp_username=${GIRDER_SMTP_USER} smtp_password=${GIRDER_SMTP_PASSWD} server_url_in_email=${SERVER_URL_IN_EMAIL} sender_address=${SENDER_ADDRESS} sample_data=${SAMPLE_DATA} session_timeout=${MIQA_SESSION_TIMEOUT}  create_assetstore=${GIRDER_CREATE_ASSETSTORE:-true} create_collection=${GIRDER_CREATE_COLLECTION:-true}",
       ]
 
   smtp-relay:
-    image: hongkongkiwi/postfix-smtp-relay:latest
+    image: boky/postfix:latest
     links:
       - web_server
     environment:
diff --git a/devops/docker/entrypoint.sh b/devops/docker/entrypoint.sh
index 54d7f53..c80cadc 100644
--- a/devops/docker/entrypoint.sh
+++ b/devops/docker/entrypoint.sh
@@ -1,4 +1,12 @@
-# Run provisioning in the background
-ansible-playbook -v --extra-vars "$2" /provision.yml &
-# start girder server
-girder serve --host 0.0.0.0 --database mongodb://"$1"/girder
+#!/bin/sh
+set -e
+
+girder serve --host 0.0.0.0 --database mongodb://"$1"/girder &
+GIRDER_PID=$!
+
+ansible-playbook -v --extra-vars "$2" /provision.yml
+
+kill "$GIRDER_PID"
+wait "$GIRDER_PID" || true
+
+exec girder serve --host 0.0.0.0 --database mongodb://"$1"/girder
diff --git a/devops/docker/provision.yml b/devops/docker/provision.yml
index 19a877d..9b56aff 100644
--- a/devops/docker/provision.yml
+++ b/devops/docker/provision.yml
@@ -53,6 +53,7 @@
       - "Collaborator"
 
   - name: Ensure Default Assetstore
+    when: create_assetstore | default(true) | bool
     girder:
       host: "localhost"
       port: "8080"
@@ -66,6 +67,7 @@
       state: present
 
   - name: Ensure Default Collection
+    when: create_collection | default(true) | bool
     girder:
       host: "localhost"
       port: "8080"
diff --git a/server/miqa_server/__init__.py b/server/miqa_server/__init__.py
index 2612080..f883ed5 100644
--- a/server/miqa_server/__init__.py
+++ b/server/miqa_server/__init__.py
@@ -1,4 +1,7 @@
 import datetime
+import smtplib
+from girder import logger
+from girder.utility import mail_utils
 from girder import events, plugin
 from girder.models.user import User
 from girder.utility import server
@@ -22,4 +25,38 @@ def load(self, info):
         info['apiRoot'].miqa_email = Email()
         info['apiRoot'].miqa_setting = SettingResource()
 
+        _orig_init = smtplib.SMTP.__init__
+
+        def debug_smtp_init(self, *args, **kwargs):
+            _orig_init(self, *args, **kwargs)
+            self.set_debuglevel(1)
+
+        smtplib.SMTP.__init__ = debug_smtp_init
+
+        original_send = mail_utils._SMTPConnection.send
+        original_enter = mail_utils._SMTPConnection.__enter__
+
+        def debug_enter(self):
+            logger.info(
+                'SMTP debug: connecting host=%r port=%r encryption=%r username=%r',
+                self.host, self.port, self.encryption, self.username
+            )
+            return original_enter(self)
+
+        def debug_send(self, fromAddress, toAddresses, message):
+            logger.info(
+                'SMTP debug: sending from=%r to=%r message_len=%d',
+                fromAddress, toAddresses, len(message)
+            )
+            try:
+                result = original_send(self, fromAddress, toAddresses, message)
+                logger.info('SMTP debug: sendmail completed: %r', result)
+                return result
+            except Exception:
+                logger.exception('SMTP debug: sendmail failed')
+                raise
+
+        mail_utils._SMTPConnection.__enter__ = debug_enter
+        mail_utils._SMTPConnection.send = debug_send
+
 server.getStaticRoot = lambda: 'static'
diff --git a/server/miqa_server/email.py b/server/miqa_server/email.py
index 917313c..d164214 100644
--- a/server/miqa_server/email.py
+++ b/server/miqa_server/email.py
@@ -56,9 +56,15 @@ def sendEmail(self, message, params):
         alternative.attach(MIMEText(''.join(
             [('<p>%s</p>' % line) for line in body.splitlines()])+'<br />'+'<br />'.join(images_html), 'html'))
 
+        to = message.get('to', [])
+        cc = message.get('cc', [])
+        bcc = message.get('bcc', [])
+
+        print("MIQA EMAIL ROUTE HIT", msg['From'], list(set(to) | set(cc) | set(bcc)), flush=True)
+
         events.daemon.trigger('_sendmail', info={
             'message': msg,
-            'recipients': list(set(message['to']) | set(message['cc']) | set(message['bcc']))
+            'recipients': list(set(to) | set(cc) | set(bcc))
         })
 
 
diff --git a/server/setup.py b/server/setup.py
index e67d531..5fc929e 100644
--- a/server/setup.py
+++ b/server/setup.py
@@ -4,6 +4,7 @@
 from setuptools import setup, find_packages
 
 requirements = [
+    'setuptools_scm==7.1.0',
     'cryptography==3.2.1',
     'girder==3.1.4',
     'girder_jobs==3.1.4',

From 07e06c577ea03d8865fef5210b7f618db7a40aaf Mon Sep 17 00:00:00 2001
From: Jim Klo <jimklo@stanford.edu>
Date: Wed, 17 Jun 2026 06:34:20 +0000
Subject: [PATCH 2/2] added option to create collections and assetstore

---
 devops/docker/.env.template | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/devops/docker/.env.template b/devops/docker/.env.template
index 9d10ccf..e3b9d87 100644
--- a/devops/docker/.env.template
+++ b/devops/docker/.env.template
@@ -2,6 +2,8 @@ COMPOSE_PROJECT_NAME=miqa
 GIRDER_ADMIN_NAME=
 GIRDER_ADMIN_PASS=
 GIRDER_API_ROOT=/api/v1
+GIRDER_CREATE_ASSETSTORE=true
+GIRDER_CREATE_COLLECTION=true
 GIRDER_STATIC_PUBLIC_PATH=/static
 GIRDER_SMTP_RELAY=smtp-relay
 GIRDER_SMTP_PORT=587