chris-allan’s gists

chris-allan / OmeroDatasetExport.java

Created October 4, 2011 15:48

OMERO dataset export example in Java

	import java.io.File;
	import java.io.FileOutputStream;
	import java.io.IOException;
	import java.util.Arrays;
	import java.util.List;

	import Glacier2.CannotCreateSessionException;
	import Glacier2.PermissionDeniedException;

	import omero.ServerError;

chris-allan / omero_homebrew.sh

Created October 14, 2011 08:17 — forked from joshmoore/README.md

Bootstrap script for creating and installing OMERO via Homebrew.

	#!/bin/bash

	set -e
	set -u

	DIR=$1
	shift

	OMERO_GIT=${OMERO_URL:-git://github.com/joshmoore/homebrew.git}
	OMERO_URL=${OMERO_URL:-https://github.com/joshmoore/homebrew/tarball/omero}

chris-allan / tileperf.py

Created January 25, 2012 17:51

PixelData tile performance log parsing script

	#!/usr/bin/env python
	# encoding: utf-8

	"""
	Performs various performance metrics and reports on PixelData log files.
	"""

	# Copyright (C) 2011 University of Dundee

	# This program is free software; you can redistribute it and/or

chris-allan / OmeroImport.java

Created January 31, 2012 11:59

OMERO import example in Java

	import loci.formats.in.DefaultMetadataOptions;
	import loci.formats.in.MetadataLevel;
	import ome.formats.OMEROMetadataStoreClient;
	import ome.formats.importer.ImportConfig;
	import ome.formats.importer.cli.ErrorHandler;
	import ome.formats.importer.cli.LoggingImportMonitor;
	import omero.model.Dataset;

	public class OmeroImport {

chris-allan / edit_plate.py

Created September 20, 2012 16:51

OMERO plate attribute update example in Python

	#
	# To be run in OMERO CLI shell as follows:
	#
	# # Download script to current working directory
	# omero shell --login
	# ...
	# %run -i edit_plate.py plate_id attribute value
	#
	import sys

chris-allan / pyramid.py

Created September 27, 2012 07:57

OMERO pyramid checking script

	import time

	import omero
	import omero.clients

	from omero.rtypes import unwrap

	HOST='localhost'
	PORT=4064
	USER='root'

chris-allan / omero_stats.sh

Created January 25, 2013 13:38

OMERO server stats for Images, frames and logins

	#!/bin/bash

	set -e
	set -u
	set -x

	HOSTNAME="localhost"
	DATABASE="omero"
	USER="omero-x"
	THIRTY_DAYS_AGO="$(date -d '30 days ago' '+%Y-%m-%d %H:%M:00')"

chris-allan / lock_files_in_directory.py

Last active December 11, 2015 22:48

Attempts to perform an exclusive, non-blocking lock on an open file handle to each file in a directory.

	#!/usr/bin/env python
	import traceback
	import fcntl
	import sys
	import os

	try:
	d, = sys.argv[1:]
	except ValueError:
	print 'Usage: %s <directory>' % sys.argv[0]

chris-allan / OMERO5.0DEV__3.sql

Last active December 16, 2015 07:59

OMERO5.0DEV__3 to OMERO5.0DEV__4 database upgrade script

	-- Copyright (C) 2013 Glencoe Software, Inc. All rights reserved.
	--
	-- This program is free software; you can redistribute it and/or modify
	-- it under the terms of the GNU General Public License as published by
	-- the Free Software Foundation; either version 2 of the License, or
	-- (at your option) any later version.
	--
	-- This program is distributed in the hope that it will be useful,
	-- but WITHOUT ANY WARRANTY; without even the implied warranty of
	-- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the

chris-allan / OMERO5.0DEV__4.sql

Created June 4, 2013 12:58

OMERO5.0DEV__4 to OMERO5.0DEV__5 database upgrade script

	-- Copyright (C) 2013 Glencoe Software, Inc. All rights reserved.
	--
	-- This program is free software; you can redistribute it and/or modify
	-- it under the terms of the GNU General Public License as published by
	-- the Free Software Foundation; either version 2 of the License, or
	-- (at your option) any later version.
	--
	-- This program is distributed in the hope that it will be useful,
	-- but WITHOUT ANY WARRANTY; without even the implied warranty of
	-- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the

Chris Allan chris-allan