Merge d4e90fb into 0b89f46

beaconsite/templates/beaconsite/site_detail.html

@@ -154,8 +154,6 @@ <h5 class="modal-title">Modal title</h5>
 {% block javascript %}
   {{ block.super }}
 
-  <script type="text/javascript" src="{% static 'js/vendor/axios-0.18.0.min.js' %}"></script>
-
   <script type="application/javascript">
     $(function () {
       $("#button-get-info").click(function () {

config/settings/base.py

@@ -566,6 +566,40 @@ def fixed_array_type(field):
 ENABLED_BACKEND_PLUGINS = ["timeline_backend"]
 ENABLED_BACKEND_PLUGINS += env.list("ENABLED_BACKEND_PLUGINS", None, [])
 
+# Warn about unsupported browsers (IE)
+PROJECTROLES_BROWSER_WARNING = True
+
+# Disable default CDN JS/CSS includes to replace with local files.  This
+# is primarily used for Docker-based deployments.
+PROJECTROLES_DISABLE_CDN_INCLUDES = env.bool("PROJECTROLES_DISABLE_CDN_INCLUDES", False)
+
+if PROJECTROLES_DISABLE_CDN_INCLUDES:
+    PROJECTROLES_CUSTOM_JS_INCLUDES = [
+        "/static/local/js/jquery-3.5.1.min.js",
+        "/static/local/js/tether.min.js",
+        "/static/local/js/shepherd.min.js",
+        "/static/local/js/clipboard.min.js",
+        "/static/local/js/bundle.tracing.min.js",
+        "/static/local/js/jquery.dataTables.min.js",
+        "/static/local/js/bootstrap-select.min.js",
+        "/static/local/js/tagsinput.js",
+        "/static/local/js/jsrender.min.js",
+        "/static/local/js/plotly-1.54.5.min.js",
+        "/static/local/js/axios.min.js",
+        "/static/local/js/palette.min.js",
+        "/static/local/js/lodash.min.js",
+    ]
+    PROJECTROLES_CUSTOM_CSS_INCLUDES = [
+        "/static/local/css/font-awesome.min.css",
+        "/static/local/css/bootstrap.min.css",
+        "/static/local/css/bootstrap-select.min.css",
+        "/static/local/css/dataTables.jqueryui.min.css",
+        "/static/local/css/tagsinput.css",
+    ]
+else:
+    PROJECTROLES_CUSTOM_JS_INCLUDES = []
+    PROJECTROLES_CUSTOM_CSS_INCLUDES = []
+
 
 def set_logging(debug):
     return {

config/settings/production.py

@@ -27,9 +27,6 @@
 # This ensures that Django will be able to detect a secure connection
 # properly on Heroku.
 SECURE_PROXY_SSL_HEADER = ("HTTP_X_FORWARDED_PROTO", "https")
-# raven sentry client
-# See https://docs.sentry.io/clients/python/integrations/django/
-INSTALLED_APPS += ["raven.contrib.django.raven_compat"]
 
 # Use Whitenoise to serve static files
 # See: https://whitenoise.readthedocs.io/
@@ -89,6 +86,11 @@
 # ------------------------
 STATICFILES_STORAGE = "whitenoise.storage.CompressedManifestStaticFilesStorage"
 
+# Add Samplesheets vue.js app assets
+STATICFILES_DIRS.append(str(ROOT_DIR("varfish/vueapp/dist")))
+
+# Add optonal custom directory for static includes at deployment stage
+STATICFILES_DIRS += env.list("CUSTOM_STATIC_DIR", default=[])
 
 # EMAIL CONFIGURATION
 # ------------------------------------------------------------------------------

config/wsgi.py

@@ -23,9 +23,6 @@
 app_path = os.path.dirname(os.path.abspath(__file__)).replace("/config", "")
 sys.path.append(os.path.join(app_path, "varfish"))
 
-if os.environ.get("DJANGO_SETTINGS_MODULE") == "config.settings.production":
-    from raven.contrib.django.raven_compat.middleware.wsgi import Sentry
-
 # We defer to a DJANGO_SETTINGS_MODULE already in the environment. This breaks
 # if running multiple sites in the same mod_wsgi process. To fix this, use
 # mod_wsgi daemon mode with each site in its own daemon process, or use
@@ -36,8 +33,7 @@
 # file. This includes Django's development server, if the WSGI_APPLICATION
 # setting points here.
 application = get_wsgi_application()
-if os.environ.get("DJANGO_SETTINGS_MODULE") == "config.settings.production":
-    application = Sentry(application)
+
 # Apply WSGI middleware here.
 # from helloworld.wsgi import HelloWorldApplication
 # application = HelloWorldApplication(application)

docker/Dockerfile

@@ -4,6 +4,7 @@ ARG app_git_url=https://github.com/bihealth/varfish-server.git
 ARG app_git_tag
 
 ENV DEBIAN_FRONTEND noninteractive
+ENV CUSTOM_STATIC_DIR /usr/src/app/local-static
 
 ## Add the wait script to the image
 ADD https://github.com/ufoscout/docker-compose-wait/releases/download/2.7.3/wait /usr/local/bin/wait
@@ -16,14 +17,14 @@ RUN git clone --depth 1 --branch $app_git_tag $app_git_url /usr/src/app
 # Install system dependencies.
 RUN apt-get update && \
     apt-get install -y \
-        apt-utils
-RUN apt-get install -y \
+        apt-utils \
         gcc \
         ldap-utils \
         libldap2-dev \
         libsasl2-dev \
         make \
-        postgresql-client
+        postgresql-client \
+        wget
 
 # Install Python dependencies.
 RUN cd /usr/src/app && \
@@ -38,6 +39,43 @@ RUN curl -sL https://deb.nodesource.com/setup_12.x | bash - && \
 RUN cd /usr/src/app/varfish/vueapp && \
     npm ci
 
+# Download files from CDN.
+RUN mkdir -p /usr/src/app/local-static/local/css && \
+    mkdir -p /usr/src/app/local-static/local/fonts && \
+    mkdir -p /usr/src/app/local-static/local/js && \
+    cd /usr/src/app/local-static/local/fonts && \
+    wget \
+        https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/fonts/FontAwesome.otf \
+        https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/fonts/fontawesome-webfont.eot \
+        https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/fonts/fontawesome-webfont.svg \
+        https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/fonts/fontawesome-webfont.ttf \
+        https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/fonts/fontawesome-webfont.woff \
+        https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/fonts/fontawesome-webfont.woff2 && \
+    \
+    cd /usr/src/app/local-static/local/css && \
+    wget \
+        https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css \
+        https://cdn.jsdelivr.net/npm/bootstrap@4.5.3/dist/css/bootstrap.min.css \
+        https://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.13.18/css/bootstrap-select.min.css \
+        https://cdn.datatables.net/1.10.24/css/dataTables.jqueryui.min.css \
+        https://cdn.jsdelivr.net/npm/bootstrap4-tagsinput@4.1.3/tagsinput.css && \
+    \
+    cd /usr/src/app/local-static/local/js && \
+    wget \
+        https://code.jquery.com/jquery-3.5.1.min.js \
+        https://cdnjs.cloudflare.com/ajax/libs/tether/1.4.4/js/tether.min.js \
+        https://cdnjs.cloudflare.com/ajax/libs/shepherd/1.8.1/js/shepherd.min.js \
+        https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.0/clipboard.min.js \
+        https://browser.sentry-cdn.com/6.2.5/bundle.tracing.min.js \
+        https://cdn.datatables.net/1.10.24/js/jquery.dataTables.min.js \
+        https://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.13.18/js/bootstrap-select.min.js \
+        https://cdn.jsdelivr.net/npm/bootstrap4-tagsinput@4.1.3/tagsinput.js \
+        https://cdnjs.cloudflare.com/ajax/libs/jsrender/1.0.11/jsrender.min.js \
+        https://cdn.plot.ly/plotly-1.54.5.min.js \
+        https://cdnjs.cloudflare.com/ajax/libs/axios/0.21.1/axios.min.js \
+        https://cdnjs.cloudflare.com/ajax/libs/google-palette/1.1.0/palette.min.js \
+        https://cdnjs.cloudflare.com/ajax/libs/lodash.js/4.17.21/lodash.min.js
+
 # Prepare static files
 RUN cd /usr/src/app && \
     mkdir -p /usr/src/app/varfish/vueapp/dist && \

requirements/base.txt

@@ -119,8 +119,6 @@ django-su
 # Sentry client.
 sentry-sdk ==0.14.0
 
-raven ==6.10.0
-
 # Redis support
 redis==3.3.8
 

requirements/local.txt

@@ -9,6 +9,8 @@ django-debug-toolbar-alchemy==0.1.5
 
 # improved REPL
 ipdb==0.13.4, <0.14
+# downgrade jedi to fix tb_frame problem
+jedi==0.17.2
 
 pytest-django==3.4.2
 pytest-sugar==0.9.1

svs/templates/svs/scripts.html

@@ -30,7 +30,6 @@
   let variant_flags_url = "{% url 'svs:sv-flags-api' project=project.sodar_uuid case="--abcef--" sv="--bbccee--" %}";
   let variant_comment_url = "{% url 'svs:sv-comment-api' project=project.sodar_uuid case="--abcef--" sv="--bbccee--" %}";
 </script>
-<script type="text/javascript" src="{% static "js/vendor/lodash-4.17.15.min.js" %}"></script>
 <script type="text/javascript" src="{% static "js/helpers.js" %}"></script>
 <script type="text/javascript" src="{% static "js/filter_form.js" %}"></script>
 <script type="text/javascript" src="{% static "js/flags_comments.js" %}"></script>