omero.properties

#
# omero.properties
# -----------------
#
# This properties file is compiled into blitz.jar and serves as a default
# for all values server-side values (client configuration happens differently).
# Any of these properties can be altered by using bin/omero config. This filel
# can and should not be modified. Instead, new properties are set in
#
#   etc/grid/config.xml
#

omero.data.dir=/OMERO/
omero.managed.dir=${omero.data.dir}/ManagedRepository
omero.data.cron=* * 0 * * ?

omero.db.authority=export.openmicroscopy.org
omero.db.version=OMERO5.0
omero.db.patch=0
omero.db.host=localhost
omero.db.name=omero
omero.db.user=omero
omero.db.pass=omero
omero.db.poolsize=10
omero.db.prepared_statement_cache_size=10

# Default values for the current profile will be
# hard-coded into the hibernate.properties file
# in the model-*.jar. By using a different jar,
# you can modify the defaults.
#
# Note: some other properties are defined in
# the file etc/profiles/${omero.db.profile}
# Especially of importance is omero.db.port
omero.db.profile=psql

# Whether JMX statistics are collected
# for DB usage (by Hibernate, etc)
omero.db.statistics=true

omero.security.chmod_strategy=groupChmodStrategy
omero.security.filter.bitand=(int8and(permissions,%s) = %s)
omero.security.password_provider=chainedPasswordProvider
omero.security.login_failure_throttle_count=1
omero.security.login_failure_throttle_time=3000
omero.security.keyStore=
omero.security.keyStorePassword=
omero.security.trustStore=
omero.security.trustStorePassword=


############################################
# upgrade check:
# -------------
# On each startup the OMERO server checks
# the defined url for possible upgrades.
#
# If you would like to disable the checks,
# set the url to an empty string.
#
# For more information, see
# http://trac.openmicroscopy.org.uk/ome/wiki/UpgradeCheck
#
############################################
omero.upgrades.url=http://upgrade.openmicroscopy.org.uk
omero.upgrades.poll=0

############################################
# appserver product (ear) configuration
############################################
product.name=OMERO.server
product.license="GNU GPL, version 2"
product.final.name=omero.ear

############################################
# OMERO.scripts properties
############################################
# No value implies use sys.executable
omero.launcher.python=
omero.launcher.jython=jython
omero.launcher.matlab=matlab
omero.process.python=omero.processor.ProcessI
omero.process.jython=omero.processor.ProcessI
omero.process.matlab=omero.processor.MATLABProcessI

############################################
# server configuration
#
# Cron Format: seconds minutes hours day-of-month month day-of-week year(optional)
#
# For example, "0,30 * * * * ?" is equivalent to running
# every 30 seconds. For more information, see:
# http://quartz.sourceforge.net/javadoc/org/quartz/CronTrigger.html
############################################

# To disable pixelsdata processing, leave blank.
omero.pixeldata.cron=*/4 * * * * ?

# How many pixel pyramids will be generated
# at a single time. The value should typically
# not be set to higher than the number of
# cores on the server machine.
omero.pixeldata.threads=2

# Number of instances indexed per indexing.
# Larger batches can speed up indexing, but
# at the cost of memory.
omero.pixeldata.batch=50

# Instead, it is possible to tell the server
# to run more pixeldata reptitions, each of
# which gets completely committed before the
# next. This will only occur when there is
# a substantial backlog of pixels to process.
#
omero.pixeldata.repetitions=1

# Name of the spring bean which will be used
# to calculate the backoff (in ms) that users
# should wait for an image to be ready to view.
omero.pixeldata.backoff=ome.io.nio.SimpleBackOff
# Maximum time in milliseconds that file parsing
# can take without the parsed metadata being
# cached to BioFormatsCache.
omero.pixeldata.memoizer_wait=100

# Whether the PixelData.dispose() method should
# try to clean up ByteBuffer instances which may
# lead to memory exceptions. See ticket #11675
# for more information. Note: the property is
# set globally for the JVM.
omero.pixeldata.dispose=false

# Default sizes for tiles are provided by a
# ome.io.nio.TileSizes implementation. By default
# the bean ("configuredTileSizes") uses the properties
# provided here.
omero.pixeldata.tile_sizes_bean=configuredTileSizes
omero.pixeldata.tile_width=256
omero.pixeldata.tile_height=256
omero.pixeldata.max_plane_width=3192
omero.pixeldata.max_plane_height=3192

# To disable search indexing, leave blank.
omero.search.cron=*/4 * * * * ?

# Number of instances indexed per indexing.
# Larger batches can speed up indexing, but
# at the cost of memory.
omero.search.batch=50

# Instead, it is possible to tell the server
# to run more indexing reptitions, each of
# which gets completely committed before the
# next. This will only occur when there is
# a substantial backlog of searches to perform.
# (More than 1 hours worth)
#
omero.search.repetitions=1

# Analyzer used both index and to parse queries
omero.search.analyzer=ome.services.fulltext.FullTextAnalyzer

# Maximum number of OR-clauses to which a single search can expand
omero.search.maxclause=4096

# Maximum file size for text indexing
# This should not be set to more than half of the Indexer heap space.
# By default, 125 MB.
omero.search.max_file_size=131072000

# Indexing takes place on all EventLogs as they occur in the database.
# The types listed here will be skipped if they appear in the "entityType"
# field of the EventLog table.
omero.search.excludes=\
ome.model.annotations.ChannelAnnotationLink,\
ome.model.core.Channel,ome.model.core.PlaneInfo,ome.model.core.PixelsOriginalFileMap,\
ome.model.containers.DatasetImageLink,ome.model.containers.ProjectDatasetLink,\
ome.model.containers.CategoryGroupCategoryLink,ome.model.containers.CategoryImageLink,\
ome.model.display.ChannelBinding,ome.model.display.QuantumDef,\
ome.model.display.Thumbnail,\
ome.model.meta.Share,ome.model.meta.Event,ome.model.meta.EventLog,ome.model.meta.GroupExperimenterMap,\
ome.model.meta.Node,ome.model.meta.Session,\
ome.model.annotations.RoiAnnotationLink,ome.model.roi.Roi,ome.model.roi.Shape,ome.model.roi.Text,\
ome.model.roi.Rect,ome.model.roi.Mask,ome.model.roi.Ellipse,ome.model.roi.Point,\
ome.model.roi.Path,ome.model.roi.Polygon,ome.model.roi.Polyline,ome.model.roi.Line\
ome.model.screen.ScreenAcquisitionWellSampleLink,ome.model.screen.ScreenPlateLink,ome.model.screen.WellReagentLink,\
ome.model.stats.StatsInfo

# Extra bridge classes, comma-separated, to be invoked on each indexing.
# Bridges are used to parse more information out of the data.
omero.search.bridges=

omero.search.locking_strategy=native

# For more information, see:
# http://trac.openmicroscopy.org.uk/ome/wiki/OmeroSearch

# Template for FS managed repository paths.
# Allowable elements are:
# %user%       bob
# %userId%     4
# %group%      bobLab
# %year%       2011
# %month%      01
# %monthname%  january
# %day%        01
# %time%       15-13-54.014
# /            path separator
#
# %user%_%userId%/ must come first, and the path must be unique per fileset
# to prevent upload conflicts, which is why %time% includes milliseconds.
#
# The template path is created below <omero.managed.dir>,
# e.g. /OMERO/ManagedRepository/<omero.fs.repo.path>/
omero.fs.repo.path=%user%_%userId%/%year%-%month%/%day%/%time%

# Rules to apply to judge the acceptability of FS paths for writing into
# omero.managed.dir, being any comma-separated non-empty subset of:
#  - Windows required
#  - Windows optional
#  - UNIX required
#  - UNIX optional
# Minimally, the "required" appropriate for the server is recommended.
# Also applying optional rules may make sysadmin tasks easier,
# but may be more burdensome for users who name their files oddly.
omero.fs.repo.path_rules=Windows required, UNIX required

# Checksum algorithms supported by the server for new file uploads,
# being any comma-separated non-empty subset of:
#  - Adler-32
#  - CRC-32
#  - MD5-128
#  - Murmur3-32
#  - Murmur3-128
#  - SHA1-160
# In negotiation with clients, this list is interpreted as being in
# descending order of preference.
omero.checksum.supported=SHA1-160, MD5-128, Murmur3-128, Murmur3-32, CRC-32, Adler-32

############################################
# session configuration
#
# timeout values are in milliseconds to make
# comparison with start/finish values more
# straightforward
############################################
omero.sessions.timeout=600000
omero.sessions.maximum=0
omero.sessions.sync_interval=120000
omero.sessions.sync_force=1800000

############################################
# threading configuring
#
# sets timeouts and thread pool information
# for internal server threads.
############################################
omero.threads.min_threads=5
omero.threads.max_threads=50
omero.threads.idle_timeout=5000
omero.threads.cancel_timeout=5000

############################################
# throttling configuration
#
# timeout values are in milliseconds to make
# comparison with start/finish values more
# straightforward
# http://trac.openmicroscopy.org.uk/ome/wiki/OmeroThrottling
############################################
omero.throttling.objects_read_interval=1000
omero.throttling.objects_written_interval=1000
omero.throttling.method_time.warn=5000
omero.throttling.method_time.error=15000
omero.throttling.servants_per_session=10000


############################################
# cluster configuration
#
# http://trac.openmicroscopy.org.uk/ome/wiki/OmeroClustering
############################################
omero.cluster.redirector=nullRedirector
omero.cluster.read_only=false

############################################
# grid configuration
#
# registry_timeout is the milliseconds which
#  the registry and other services will wait
#  on remote services to respond.
#
# http://trac.openmicroscopy.org.uk/ome/wiki/OmeroGrid
############################################
omero.grid.registry_timeout=5000


############################################
# Reset password properties
############################################
omero.resetpassword.bean=defaultMailSender
omero.resetpassword.config=false
omero.resetpassword.from=ADDRESS@domain
omero.resetpassword.host=smtp.domain
omero.resetpassword.port=25
omero.resetpassword.username=
omero.resetpassword.password=
omero.resetpassword.mail.transport.protocol=smtp
omero.resetpassword.mail.smtp.auth=false
omero.resetpassword.mail.debug=false
omero.resetpassword.mail.smtp.starttls.enable=false
omero.resetpassword.mail.smtp.socketFactory.class=javax.net.SocketFactory
omero.resetpassword.mail.smtp.socketFactory.fallback=false
omero.resetpassword.mail.smtp.socketFactory.port=25
omero.resetpassword.mail.smtp.timeout=25000

############################################
# Ldap properties
############################################
omero.ldap.config=false
omero.ldap.urls=ldap://localhost:389
omero.ldap.username=
omero.ldap.password=
omero.ldap.base=ou=example,o=com
omero.ldap.referral=ignore

# Whether or not values from LDAP will be
# sychronized to OMERO on each login. This includes
# not just the user name, email, etc, but also the
# groups that the user is a member of.
#
# WARNING:
# -------------------------------------------------
#   Currently setting this to true the user will be
#   removed from any groups to which they have been
#   added outside of LDAP! Please use carefully.
#
omero.ldap.sync_on_login=false

omero.ldap.user_filter=(objectClass=person)
omero.ldap.user_mapping=omeName=cn,firstName=givenName,lastName=sn,email=mail

omero.ldap.group_filter=(objectClass=groupOfNames)
omero.ldap.group_mapping=name=cn

## Without a prefix the "new_user_group" property
## specifies the name of a single group which all
## new users will be added to.
omero.ldap.new_user_group=default

## Examples of other new_user_group strings
## The ":x: prefixes specify actions which should
## take place

## :ou: uses the final organizational unit of a user's dn
## as the single OMERO group
## omero.ldap.new_user_group=:ou:

## :attribute: uses all the values of the specified
## attribute as the name of multiple OMERO groups.
## omero.ldap.new_user_group=:attribute:memberOf

## Like :attribute:, :filtered_attribute: uses all the
## values of the specified attribute as the name of
## multiple OMERO groups but the attribute must pass
## the same filter as :query: does.
## omero.ldap.new_user_group=:filtered_attribute:memberOf

## Similar to :attribute:, :dn_attribute: uses all the
## values of the specified attribute as the DN of
## multiple OMERO groups.
## omero.ldap.new_user_group=:dn_attribute:memberOf

## A combination of filtered_attribute and dn_attribute,
## :filtered_dn_attribute: uses all of the values of the
## specificied attribute as the DN of multipl OMERO groups
## but the attribute must pass the same filter as :query:
## omero.ldap.new_user_group=:filtered_dn_attribute:memberOf

## :query: performs a query for groups. The "name"
## property will be taken as defined by omero.ldap.group_mapping
## and the resulting filter will be AND'ed with the value
## group_filter (above)
## omero.ldap.new_user_group=:query:(member=@{dn})

## :bean: looks in the server's context for a
## bean with the given name which implements ome.security.auth.NewUserGroupBean
## omero.ldap.new_user_group=:bean:myNewUserGroupMapperBean

############################################
# Library versions
############################################
versions.ome-java=2007-Aug-07-r3052
##
versions.JHotDraw=7.0.9
versions.TableLayout=bin-jdk1.5-2009-08-26
versions.ai_path=20110331
versions.apacheds=1.5.6
versions.activation=1.1.1
versions.ant=1.8.0
versions.antlr=2.7.6
versions.asm=1.5.3
versions.axis=1.4
versions.backport=Java50-3.1
versions.batik=1.8pre-jdk6
versions.btm=2.1.3
versions.cglib=2.2
versions.checkstyle=4.3
versions.clients-util=r7223-b1483
versions.commons-beanutils=1.8.0
versions.commons-codec=1.6
versions.commons-collections=3.2
versions.commons-digester=1.8
versions.commons-discovery=0.2
versions.commons-httpclient=3.1
versions.commons-io=1.4
versions.commons-lang=2.5
versions.commons-logging=1.1.1
versions.commons-pool=1.2
versions.commons-validator=1.3.1
versions.dom4j=1.6.1
versions.ehcache=2.1.0
versions.emma=2.0.5312
versions.findbugs=1.2.1
versions.forms=1.2.1
versions.gicentreUtils=20110331
versions.gtkjfilechooser=1.4.8
versions.guava=13.0
versions.hibernate-search=3.1.1.GA
versions.hibernate-tools=3.2.0.beta11
versions.hibernate-validator=3.1.0.GA
versions.hibernate=3.5.6-4510
versions.i5d=1.2.0
versions.ice33=3.3.1
versions.ice33_lib=33
versions.ice34=3.4.2
versions.ice34_lib=34
versions.ice35=3.5.1
versions.ice35_lib=35
versions.ij=1.41
versions.ipython=0.10.1
versions.jakarta-oro=2.0.8
versions.jaxrpc=1.1
versions.jamon=2.7
versions.janino=2.5.10
versions.jarbundler=2.1.0
versions.javassist=3.9.0.GA
versions.java-image-scaling=0.8.5
versions.jcommon=1.0.14
versions.jfreechart=1.0.11
versions.jogl=1.1.1
versions.jsch=0.1.25
versions.jta=1.0.1B
versions.jts=1.10
versions.log4j=1.2.17
versions.logback=1.0.9
# Change url in antlib/resources/release.xml when changing lucene version
versions.lucene=2.4.1
versions.mail=1.4.1
versions.nanoxml=2.2.3
versions.nsisant=1.2
versions.ols-client=1.15
versions.perf4j=0.9.16
versions.persistence-api=1.0.0.Final
versions.processing-core=20110128
versions.processing-controlP5=20110218
versions.poi-scratchpad=3.0-rc4-20070503
versions.poi=3.6-20091214
versions.physics=20110331
versions.quartz=1.5.2
versions.reportng=1.1.1
versions.saaj=1.2
versions.shared-ldap=0.9.15
versions.slf4j=1.7.2
versions.spring=3.0.1.RELEASE-A
versions.spring-ldap=1.3.0.RELEASE
versions.spring-security=3.0.2.RELEASE
versions.swingx=0.9.4
versions.robotframework.swinglibrary=1.6.0a
versions.tablelayout=bin-jdk1.5-2009-08-26
versions.testng=6.8
versions.tyrex=1.0.3
versions.velocity-tools=1.1
versions.velocity=1.4
versions.wsdl4j=1.5.1
versions.xercesImpl=2.6.2
versions.xml-apis=1.3.02
versions.xmlParserAPIs=2.6.2
versions.FontBox=0.1.0
versions.PDFBox=0.7.3
versions.xalan=2.7.1
versions.jna=3.4.0
versions.platform=3.4.0

###
### Appended Values
###