Merge branch 'master' into...

Merge branch 'master' into 2021-04-02T17.33.12-branched_from_master-Adjustments_for_attribute_wrapper

docker-compose/jupyter.yml

@@ -26,6 +26,7 @@ services:
       - DISPLAY=${DISPLAY}
     ports:
       - "8888:8888"
+    user: ${CONTAINER_EXECUTION_UID}
     working_dir: /jupyter-notebooks
     entrypoint:
       - /usr/local/bin/wait-for-it.sh
@@ -33,5 +34,5 @@ services:
       - --timeout=30
       - --strict
       - --
-      - /usr/bin/tini -- jupyter notebook --port=8888 --no-browser --ip=0.0.0.0 --allow-root --NotebookApp.token= --NotebookApp.password=
+      - /usr/bin/tini -- /usr/local/bin/jupyter-notebook --port=8888 --no-browser --ip=0.0.0.0 --allow-root --NotebookApp.token= --NotebookApp.password=
     restart: on-failure

docker-compose/jupyter/Dockerfile

 ARG VERSION=latest
 FROM nexus.engageska-portugal.pt/ska-docker/tango-itango:${VERSION}
 
-RUN pip3 install jupyter
-RUN pip3 install ipykernel
-RUN pip3 install jupyter_bokeh
+RUN sudo pip3 install jupyter
+RUN sudo pip3 install ipykernel
+RUN sudo pip3 install jupyter_bokeh
 
 # Configure jupyter_bokeh
 RUN sudo mkdir -p /usr/share/jupyter /usr/etc
 RUN sudo chmod a+rwx /usr/share/jupyter /usr/etc
-RUN jupyter nbextension install --sys-prefix --symlink --py jupyter_bokeh
-RUN jupyter nbextension enable jupyter_bokeh --py --sys-prefix
+RUN sudo jupyter nbextension install --sys-prefix --symlink --py jupyter_bokeh
+RUN sudo jupyter nbextension enable jupyter_bokeh --py --sys-prefix
 
 # Install profiles for ipython & jupyter
 COPY ipython-profiles /opt/ipython-profiles/
 RUN sudo chown tango.tango -R /opt/ipython-profiles
 COPY jupyter-kernels /usr/local/share/jupyter/kernels/
 
+# Install patched jupyter executable
+RUN sudo pip3 install python-logstash-async
+COPY jupyter-notebook /usr/local/bin/jupyter-notebook
+
 # Add Tini. Tini operates as a process subreaper for jupyter. This prevents kernel crashes.
 ENV TINI_VERSION v0.6.0
+ENV JUPYTER_RUNTIME_DIR=/tmp
 ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /usr/bin/tini
 RUN sudo chmod +x /usr/bin/tini

docker-compose/jupyter/jupyter-notebook

+#!/usr/bin/python3
+# -*- coding: utf-8 -*-
+# An adjustment of the `jupyter-notebook' executable patched to:
+#  - log to the ELK stack
+#
+# We go straight for the notebook executable here, as the "jupyter" command
+# execvp's into the requested notebook subcommand, erasing all configuration
+# we set here.
+import re
+import sys
+
+from notebook.notebookapp import main 
+
+from logstash_async.handler import AsynchronousLogstashHandler, LogstashFormatter
+import logging
+
+if __name__ == '__main__':
+    # log to the tcp_input of logstash in our ELK stack
+    handler = AsynchronousLogstashHandler("elk", 5959, database_path='/tmp/pending_log_messages.db')
+
+    # add to logger of Jupyter traitlets Application. As that logger is configured not to propagate
+    # messages upward, we need to configure it directly.
+    logger = logging.getLogger("NotebookApp")
+    logger.addHandler(handler)
+    logger.setLevel(logging.DEBUG)
+
+    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
+    sys.exit(main())

docker-compose/lofar-device-base/Dockerfile

 FROM nexus.engageska-portugal.pt/ska-docker/tango-itango:latest
 
 COPY lofar-requirements.txt /lofar-requirements.txt
-RUN pip3 install -r /lofar-requirements.txt
+RUN sudo pip3 install -r /lofar-requirements.txt
+
+ENV TANGO_LOG_PATH=/var/log/tango
+RUN sudo mkdir -p /var/log/tango && sudo chmod a+rwx /var/log/tango

docker-compose/lofar-device-base/lofar-requirements.txt

 opcua >= 0.98.9
-astropy 
+astropy
+python-logstash-async