omero-server.properties

##
## omero-server.properties
## -----------------------
##
## DO NOT EDIT!
##
## This properties file is compiled into omero-server.jar and serves as a default
## for all server-side values (client configuration happens differently).
##
## Any of these properties can be altered by using bin/omero config. MODIFYING
## THIS FILE DOES NOT ALTER SERVER BEHAVIOR. It solely defines the defaults
## at compile time!
##
## For an overview of these properties, see
## https://docs.openmicroscopy.org/latest/omero/sysadmins/config.html
##
## Properties marked with "DEVELOPMENT" should not be used in production.

#########################################################
## Policies & restrictions
#########################################################

# Instance of the PolicyService interface which
# will be responsible for checking certain server
# actions made by a user.
omero.policy.bean=defaultPolicyService

# Configuration for the policy of whether users
# can access binary files from disk. Binary access
# includes all attempts to download a file from the
# UI.
#
# The individual components of the string include:
#
# - write - whether or not users who have WRITE
#   access to the objects can access the binary.
#   This includes group and system administrators.
#
# - read - whether or not users who have READ
#   access to the objects can access the binary.
#
# - image - whether or not images are to be considered
#   accessible as a rule.
#
# - plate - whether or not plates and contained HCS
#   objects are to be considered accessible as a rule.
#   This includes wells, well samples, and plate runs.
#
# Though the order of the components of the property
# are not important, the order that they are listed above
# roughly corresponds to their priority. E.g. a -write
# value will override +plate.
#
# Example 1: "-read,+write,+image,-plate" only owners
# of an image and admins can download it.
#
# Example 2: "-read,-write,-image,-plate" no downloading
# is possible.
#
# Configuration properties of the same name can be applied
# to individual groups as well. E.g. adding,
# omero.policy.binary_access=-read to a group, you can
# prevent group-members from downloading original files.
#
# Configuration is pessimistic: if there is a negative
# *either* on the group *or* at the server-level, the
# restriction will be applied. A missing value at the
# server restricts the setting but allows the server
# to override.
#
omero.policy.binary_access=+read,+write,+image


#############################################
## OMERO.scripts properties
#############################################
omero.scripts.timeout=3600000

# Executable on the PATH which will be used for scripts
# with the mimetype 'text/x-python'.
#
# No value implies use sys.executable
omero.launcher.python=

# Executable on the PATH which will be used for scripts
# with the mimetype 'text/x-jython'.
omero.launcher.jython=jython

# Executable on the PATH which will be used for scripts
# with the mimetype 'text/x-matlab'.
omero.launcher.matlab=matlab

# Server implementation which will be used for scripts
# with the mimetype 'text/x-python'. Changing this value
# requires that the appropriate class has been installed
# on the server.
omero.process.python=omero.processor.ProcessI

# Server implementation which will be used for scripts
# with the mimetype 'text/x-jython'. Changing this value
# requires that the appropriate class has been installed
# on the server.
omero.process.jython=omero.processor.ProcessI

# Server implementation which will be used for scripts
# with the mimetype 'text/x-matlab'. Changing this value
# requires that the appropriate class has been installed
# on the server.
omero.process.matlab=omero.processor.MATLABProcessI

# Frequency to reload script params. By default,
# once a day at midnight.
#
# |cron|
omero.scripts.cache.cron=0 0 0 * * ?

# Guava LoadingCache spec for configuring how
# many script JobParams will be kept in memory
# for how long.
#
# For more information, see
# https://google.github.io/guava/releases/27.1-jre/api/docs/com/google/common/cache/CacheBuilderSpec.html
omero.scripts.cache.spec=maximumSize=1000

#############################################
## server configuration
##
##
#############################################

# Which bean to use:
# nullMetrics does nothing
# defaultMetrics uses the properties defined below
omero.metrics.bean=defaultMetrics

# Address for Metrics to send server data
omero.metrics.graphite=

# Number of minutes to periodically print to slf4j
# 0 or lower disables the printout.
omero.metrics.slf4j_minutes=60


#############################################
## Query configuration
#############################################

# For the query service how many seconds before a query times out.
omero.query.timeout=1000

# How many seconds before a query times out for administrative users.
omero.query.timeout.admin=${omero.query.timeout}


#############################################
## Search properties
##
## For more information, see
## https://docs.openmicroscopy.org/latest/omero/developers/Modules/Search.html
#############################################

# Polling frequency of the indexing. Set empty to disable search indexing.
#
# |cron|
omero.search.cron=*/2 * * * * ?

# Size of the batches to process events per indexing.
# Larger batches can speed up indexing, but at the cost of memory.
omero.search.batch=5000

omero.search.event_log_loader=eventLogQueue

##
## New loader: "eventLogQueue"
##

# Number of objects to load in a single
# indexing window. The larger this value
# the fewer times a single object will be
# indexed unnecessarily. Each object uses
# roughly 100 bytes of memory.
omero.search.max_partition_size=1000000

# Whitelist of object types which will be
# indexed. All other types will be ignored.
# This matches the currently available UI
# options but may need to be expanded for
# custom search bridges.
omero.search.include_types=ome.model.core.Image,ome.model.containers.Project,\
ome.model.containers.Dataset,ome.model.screen.Plate,ome.model.screen.Screen,\
ome.model.screen.PlateAcquisition,ome.model.screen.Well

# EventLog.action values which will be indexed.
# Unless custom code is generating other action
# types, this property should not need to be
# modified.
omero.search.include_actions=INSERT,UPDATE,REINDEX,DELETE


##
## Old loader: "persistentEventLogLoader"
##

# Instead, it is possible to tell the server
# to run more indexing repetitions, 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

# 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.Rectangle,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

##
## Common properties
##

# Periodically the completion percentage will be printed.
# The calculation can be expensive and so is not done
# frequently.
omero.search.reporting_loops=100

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

# Maximum file size for text indexing (bytes)
# If a file larger than this is attached, e.g. to an image, the indexer will
# simply ignore the contents of the file when creating the search index.
# This should not be set to more than half of the Indexer heap space.
#
# .. note::
#   If you set the max file size to greater than 1/2 the size of the
#   indexer's heap (256 MB by default), you may encounter Out of Memory
#   errors in the Indexer process or you may cause the search index to
#   become corrupt. Be sure that you also increase the heap size accordingly
#   (see :ref:`out_of_memory_error`).
omero.search.max_file_size=131072000

# 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
omero.search.merge_factor=25
omero.search.ram_buffer_size=64


#############################################
## session configuration
##
## timeout values are in milliseconds to make
## comparison with start/finish values more
## straightforward
#############################################

# Sets the duration of inactivity in milliseconds after which
# a login is required.
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.
#############################################

# Number of threads that will be kept waiting
# at all times.
omero.threads.min_threads=5

omero.threads.idle_timeout=5000
omero.threads.cancel_timeout=5000

# Maximum number of threads that can simultaneously
# run at the "USER" priority level. Internal system
# threads may still run.
omero.threads.max_threads=50

# Number of threads from the max_threads pool that can
# be used at any given time for background tasks like
# import.
omero.threads.background_threads=10

# Number of milliseconds to wait for a slot in the
# background queue before a rejection error will be
# raised.
omero.threads.background_timeout=3600000

#############################################
## throttling configuration
##
## timeout values are in milliseconds to make
## comparison with start/finish values more
## straightforward
##
## For more information, see
## https://docs.openmicroscopy.org/latest/omero/developers/Server/Throttling.html
#############################################
omero.throttling.objects_read_interval=1000
omero.throttling.objects_written_interval=1000

# Time in milliseconds after which a single method invocation
# will print a WARN statement to the server log.
omero.throttling.method_time.warn=5000

# Time in milliseconds after which a single method invocation
# will print a ERROR statement to the server log. If ERRORs
# are frequently being printed to your logs, you may want to
# increase this value after checking that no actual problem
# exists. Values of more than 60000 (1 minute) are not advised.
omero.throttling.method_time.error=20000

omero.throttling.servants_per_session=10000

# Value for the indexer is extended to 1 hour
omero.throttling.method_time.warn.indexer=3600000
# Value for the indexer is extended to 1 day
omero.throttling.method_time.error.indexer=86400000




#############################################
## Ldap properties
#############################################

# Enable or disable LDAP (`true` or `false`).
omero.ldap.config=false

# Set the URL of the LDAP server. A |SSL| URL for this
# property would be of the form: ldaps://ldap.example.com:636
omero.ldap.urls=ldap://localhost:389

# LDAP server bind DN (if required; can be empty)
omero.ldap.username=

# LDAP server bind password (if required; can be empty)
omero.ldap.password=

# LDAP server base search DN, i.e. the filter that is applied
# to all users. (can be empty in which case any LDAP user is
# valid)
omero.ldap.base=ou=example,o=com

# Available referral options are: "ignore", "follow", or "throw"
# as per the JNDI referral documentation.
omero.ldap.referral=ignore

# Whether or not values from LDAP will be
# synchronized to OMERO on each login. This includes
# not just the username, email, etc, but also the
# groups that the user is a member of.
#
# .. note::
#    Admin actions carried out in the clients may
#    not survive this synchronization e.g. LDAP
#    users removed from an LDAP group in the UI
#    will be re-added to the group when logging in
#    again after the synchronization.
#
omero.ldap.sync_on_login=false

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

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. Other new_user_group strings are prefixed with
# ``:x:`` and specify various lookups which should take
# place to find one or more target groups for the new user.
#
# ``:ou:`` uses the final organizational unit of a user's dn
# as the single OMERO group e.g. ``omero.ldap.new_user_group=:ou:``
#
#
# ``:attribute:`` uses all the values of the specified
# attribute as the name of multiple OMERO groups. e.g.
# ``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. e.g.
# ``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. e.g.
# ``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
# specified attribute as the DN of multiple OMERO groups
# but the attribute must pass the same filter as ``:query:``
# e.g. ``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) e.g.
# ``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`` e.g.
# ``omero.ldap.new_user_group=:bean:myNewUserGroupMapperBean``
#
omero.ldap.new_user_group=default

# A query element to check if user who is being created
# via the new_user_group setting should be made a
# "manager", i.e. owner, of the queried group. E.g.
# ``omero.ldap.new_user_group_owner=(owner=@{dn})``
# will use the 'manager' attribute to set the 'owner'
# flag in the database. This query element is appended
# to any query used by new_user_group with an AND.
#
# This property is not used by new_user_group type
# 'default' and only potentially by ``:bean:``.
omero.ldap.new_user_group_owner=

# Value dynamically set during the build
omero.version=