Merge branch 'feature/dockerfile-updates' into feature/buff-worms

 Closes #373

Author: felliott

Dockerfile

@@ -1,7 +1,7 @@
-FROM python:3.6-slim-buster
+FROM python:3.13-slim
 
 # ensure unoconv can locate the uno library
-ENV PYTHONPATH /usr/lib/python3/dist-packages
+ENV PYTHONPATH=/usr/lib/python3/dist-packages
 
 RUN usermod -d /home www-data \
     && chown www-data:www-data /home \
@@ -43,9 +43,9 @@ RUN usermod -d /home www-data \
 RUN mkdir -p /code
 WORKDIR /code
 
-RUN pip install -U pip==18.1
-RUN pip install setuptools==37.0.0
-RUN pip install unoconv==0.8.2
+RUN pip install -U pip==24.0
+RUN pip install setuptools==69.5.1
+RUN pip install unoconv==0.9.0
 
 COPY ./requirements.txt /code/
 
@@ -55,7 +55,7 @@ RUN pip install --no-cache-dir -r ./requirements.txt
 COPY ./ /code/
 
 ARG GIT_COMMIT=
-ENV GIT_COMMIT ${GIT_COMMIT}
+ENV GIT_COMMIT=${GIT_COMMIT}
 
 RUN python setup.py develop
 

dev-requirements.txt

@@ -9,8 +9,8 @@ coveralls
 flake8==3.0.4
 ipdb
 mccabe
-pydevd==0.0.6
+pydevd==3.3.0
 pyflakes
 pytest==2.8.2
 pytest-cov==2.2.0
-pyzmq==14.4.1
+pyzmq==26.1.0

mfr/server/app.py

@@ -7,7 +7,10 @@
 import tornado.web
 import tornado.httpserver
 import tornado.platform.asyncio
-from raven.contrib.tornado import AsyncSentryClient
+
+import sentry_sdk
+from sentry_sdk.integrations.tornado import TornadoIntegration
+from sentry_sdk.integrations.logging import LoggingIntegration
 
 from mfr import settings
 from mfr.server import settings as server_settings
@@ -46,6 +49,15 @@ def almost_apache_style_log(handler):
 
 
 def make_app(debug):
+    sentry_logging = LoggingIntegration(
+        level=logging.INFO,  # Capture INFO level and above as breadcrumbs
+        event_level=None,  # Do not send logs of any level as events
+    )
+    sentry_sdk.init(
+        dsn=settings.SENTRY_DSN,
+        release=__version__,
+        integrations=[TornadoIntegration(), sentry_logging, ],
+    )
     app = tornado.web.Application(
         [
             (r'/static/(.*)', tornado.web.StaticFileHandler, {'path': server_settings.STATIC_PATH}),
@@ -59,7 +71,6 @@ def make_app(debug):
         debug=debug,
         log_function=almost_apache_style_log,
     )
-    app.sentry_client = AsyncSentryClient(settings.SENTRY_DSN, release=__version__)
     return app
 
 

mfr/server/handlers/core.py

@@ -7,7 +7,7 @@
 
 import tornado.web
 import tornado.iostream
-from raven.contrib.tornado import SentryMixin
+import sentry_sdk
 
 import waterbutler.core.utils
 import waterbutler.server.utils
@@ -76,7 +76,7 @@ def options(self):
             self.set_header('Access-Control-Allow-Methods', 'GET, PUT, POST, DELETE'),
 
 
-class BaseHandler(CorsMixin, tornado.web.RequestHandler, SentryMixin):
+class BaseHandler(CorsMixin, tornado.web.RequestHandler):
     """Base class for the Render and Export handlers.  Fetches the file metadata for the file
     indicated by the ``url`` query parameter and builds the provider caches.  Also handles
     writing output and errors.
@@ -159,8 +159,11 @@ async def write_stream(self, stream):
             return
 
     def write_error(self, status_code, exc_info):
-        self.captureException(exc_info)  # Log all non 2XX codes to sentry
         etype, exc, _ = exc_info
+        scope = sentry_sdk.get_current_scope()
+        scope.set_tag('class', etype.__name_)
+        scope.set_tag('status_code', status_code)
+        sentry_sdk.capture_exception(exc)  # Log all non 2XX codes to sentry
 
         if issubclass(etype, exceptions.PluginError):
             try:  # clever errors shouldn't break other things

requirements.txt

@@ -1,16 +1,16 @@
-aiohttp==0.18.4
+aiohttp==3.10.6
 chardet==2.3.0
 furl==0.4.2
 humanfriendly==2.1
-invoke==0.13.0
+invoke==2.2.0
 mako==1.0.1
-raven==5.27.0
-setuptools==37.0.0
+sentry-sdk==2.22.0
+setuptools==78.1.0
 stevedore==1.2.0
-tornado==4.3
+tornado==6.4.2
 
 # WaterButler
-git+https://github.com/CenterForOpenScience/waterbutler.git@0.38.6#egg=waterbutler
+git+https://github.com/CenterForOpenScience/waterbutler.git@feature/buff-worms
 agent==0.1.2
 google-auth==1.4.1
 
@@ -23,7 +23,7 @@ pydocx==0.7.0
 
 # Image
 olefile==0.44
-Pillow==4.3.0
+Pillow==11.0.0
 psd-tools==1.4
 
 # IPython
@@ -36,7 +36,7 @@ jinja2==2.10.1
 mistune==0.8.1
 
 # Pdf
-reportlab==3.6.5
+reportlab==4.2.4
 
 # Pptx
 # python-pptx==0.5.7
@@ -45,10 +45,10 @@ reportlab==3.6.5
 docutils==0.12
 
 # Tabular
-pandas==0.25.1
+pandas==2.2.3
 xlrd==1.0.0
-h5py==2.7.0
-scipy==0.19.1
+h5py==3.13
+scipy==1.14.1
 
 # Md
 markdown==2.6.2