atarkowska’s gists

atarkowska / curl_omero_web.sh

Created January 18, 2016 12:12

Log in to OMERO.web

	#!/bin/bash
	#

	set -u
	set -e
	set -x

	COOKIES=cookies.txt

	LOGIN_URL=https://omero.host/prefix/webclient/login/

atarkowska / test-download.sh

Last active February 3, 2016 09:54

Test download

	#!/bin/bash
	#

	set -u
	set -e
	set -x
	OMERO_HOST='https://cowfish.openmicroscopy.org/merge'
	DIRECTORY='/data/files'

	if [ -d "$DIRECTORY" ]; then

atarkowska / gene.py

Created March 15, 2016 16:13

Load all genes

	import omero
	import omero.gateway
	import time, datetime

	from omero.rtypes import *

	host = "localhost"
	port = 4064
	passwd = "SECRET"
	user = "USER"

atarkowska / gist:cbafc0e97811ae561aa02bb91b44e885

Created April 28, 2016 13:00

import error on 4064

	$ dist/bin/omero import /Users/ola/OMERO/IMAGE/DEMO/PTRE/P-TRE_1_R3D_D3D.dv --debug=DEBUG
	Previously logged in to 192.168.99.100:4064 as root
	Server: [192.168.99.100:4064]
	Username: [root]
	Password:
	Created session b851c807-efd4-462d-b57f-567daaa622c3 ([email protected]:4064). Idle timeout: 10 min. Current group: system
	2016-04-28 13:59:14,273 247 [ main] INFO ome.formats.importer.ImportConfig - OMERO Version: 5.2.2-205-5acf9b8-dirty-ice35-b1
	2016-04-28 13:59:14,287 261 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 5.1.8 revision: 9eb8da31c1f01989f439963b9cc215b4398bedd8 date: 12 February 2016
	2016-04-28 13:59:14,327 301 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: DEBUG OMERO.importer: DEBUG
	2016-04-28 13:59:14,329 303 [ main] DEBUG ome.formats.importer.ImportConfig - Loaded savedDirectory from ome.formats.importer.util.IniFileLoader@6e6c3152

atarkowska / gist:0610494b668c64abe1c2f5257325a7d9

Last active May 4, 2016 21:14

omero-grid failing

	lifesci-45789:omero-grid-docker ola$ eval "$(docker-machine env omerodev)"
	lifesci-45789:omero-grid-docker ola$ ./build.py omero-grid
	Running: docker build --build-arg OMERO_VERSION=latest -t openmicroscopy/omero-grid:latest omero-grid
	Sending build context to Docker daemon 10.75 kB
	Step 1 : FROM centos:centos7
	---> 778a53015523
	Step 2 : MAINTAINER [email protected]
	---> Using cache
	---> 068ba647d62a
	Step 3 : RUN yum -y install epel-release && curl -o /etc/yum.repos.d/zeroc-ice-el7.repo http://download.zeroc.com/Ice/3.5/el7/zeroc-ice-el7.repo && yum -y install unzip wget patch java-1.8.0-openjdk ice ice-python ice-servers python-pip numpy scipy python-matplotlib python-pillow python-tables postgresql && yum clean all

atarkowska / omero-web-cache.conf

Last active May 26, 2016 13:34

Example of omero web rendering cache for nginx

	proxy_cache_path /data/omero-cache levels=1:2 keys_zone=omero:200m inactive=30d use_temp_path=off;

	map $request_uri $skip_cache
	{
	default 1;
	"~web(client\|gateway)/(render)_*" 0;
	}

	upstream omeroweb_omero {
	...

atarkowska / test_mapannotation

Last active June 9, 2016 10:36

MapAnnotation vs NamedValue

	import omero, os
	import omero.gateway
	from omero.rtypes import *

	from omero.rtypes import unwrap

	host = "localhost"
	port = 4064
	pass = "ome"
	user = "test"

atarkowska / mapannotation_remove_duplicates

Last active July 1, 2016 15:53

Remove duplicates of MapAnnotations

	#!/usr/bin/env python
	# -- coding: utf-8 --
	#
	# Copyright (c) 2016 University of Dundee.
	#
	# This program is free software: you can redistribute it and/or modify
	# it under the terms of the GNU Affero General Public License as
	# published by the Free Software Foundation, either version 3 of the
	# License, or (at your option) any later version.
	#

atarkowska / share-group.py

Last active June 26, 2016 07:30

This is example script for https://github.com/openmicroscopy/openmicroscopy/pull/4730

atarkowska / share-group.log

Last active June 26, 2016 07:35

This is an output of OMERO CLI to prepare users and groups and then put group into share to override the default group permission making it rear-only and sharing with public user

	import omero, os

	host = "localhost"
	port = 4064
	user = "user-1"
	password = "ome"

	c = omero.client(host=host, port=port)
	s = c.createSession(user, password)

	+ echo 'create public user'
	create public user
	+ /home/omero/workspace/OMERO-server/OMERO.server/bin/omero login -u root -w omero -s localhost -p 4064
	Created session acc7b1af-82a2-4762-b9ff-a30ada1c0676 (root@localhost:4064). Idle timeout: 10 min. Current group: system
	+ /home/omero/workspace/OMERO-server/OMERO.server/bin/omero group add public --perms rwr---
	Using session acc7b1af-82a2-4762-b9ff-a30ada1c0676 (root@localhost:4064). Idle timeout: 10 min. Current group: system
	Added group public (id=3) with permissions rwr---
	+ /home/omero/workspace/OMERO-server/OMERO.server/bin/omero user add public Public User --group-name public -P ome
	Using session acc7b1af-82a2-4762-b9ff-a30ada1c0676 (root@localhost:4064). Idle timeout: 10 min. Current group: system
	Added user public (id=2) with password

Ola Tarkowska atarkowska