Simon Li manics

OMERO User Meeting 2017 AWS Workshop

What is Docker?

...an open source project to pack, ship and run any application as a lightweight container.
An abstraction layer to "containerize" any application and allow it to run on any infrastructure
Used to containerize OMERO, OMERO.web and and the additional components of OMERO.cloudarchive

JupyterLab 3.0 on Binder

Try it on Binder!

This conda environment demonstrates how to install JupyterLab extensions with conda or mamba, without any end user build or requiring Node.js.

It also installs the xeus-python kernel to enable the visual debugger sidebar by default.

Using an authenticated service in a custom template

This example embeds an authenticated request to a service into the template for /hub/home. The user may not be logged in to the service when the page is requested, so we must process the oauth login to the service in that event.

To avoid the user having to experience any of the login process, this requires:

attempting to fetch the endpoint

	# make sure crypt module in use
	sudo modprobe dm-crypt

	# Find out which drive it was with the following command:
	sudo fdisk -l

	# You must mount /dev/sda3 myvolume
	# use cryptsetup, device is accessible under /dev/mapper/myvolume
	sudo cryptsetup luksOpen /dev/sde3 myvolume

	# Copy the config locally so we don't lose it
	cp dist/etc/grid/config.xml config.xml

	# Delete all previous symlinks, so that 'clean' doesn't delete src code
	rm dist/lib/python/omeroweb
	rm dist/lib/python/omero/gateway
	rm components/tools/target/lib/python/omeroweb
	rm components/tools/target/lib/python/omero/gateway
	rm components/tools/OmeroPy/target/omero/testlib/
	rm components/tools/OmeroPy/target/omero/gateway

	from urllib.parse import urlsplit

	from tornado import gen
	from tornado.escape import url_escape
	from tornado.httputil import url_concat

	from traitlets import (
	Unicode, Integer, Dict, TraitError, List, Bool, Any,
	Type, Set, Instance, Bytes, Float,
	observe, default,

	Copyright 2020 Brian Wojtczak

	Permission is hereby granted, free of charge, to any person obtaining a
	copy of this software and associated documentation files (the "Software"),
	to deal in the Software without restriction, including without limitation
	the rights to use, copy, modify, merge, publish, distribute, sublicense,
	and/or sell copies of the Software, and to permit persons to whom the
	Software is furnished to do so, subject to the following conditions:

	The above copyright notice and this permission notice shall be included

	import matplotlib.pyplot as plt
	import numpy as np
	import omero
	from omero.gateway import BlitzGateway, ColorHolder
	from omero.model import MaskI, RoiI
	from omero.rtypes import rdouble, rint, rstring
	from skimage.filters import threshold_otsu
	from skimage.measure import label, regionprops

	OME_HOST = "merge-ci"

	#!/usr/bin/bash -xe

	cat <<EOF > "${HOME}/.config/systemd/user/zoom.slice"
	[Slice]
	AllowedCPUs=0-4
	MemoryHigh=6G
	EOF

	cat /usr/share/applications/Zoom.desktop \| sed -E 's#^(Exec=).*$#Exec=/usr/bin/systemd-run --user --slice=zoom.slice /opt/zoom/ZoomLauncher#' > "${HOME}/.local/share/applications/Zoom.desktop"