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Note

This documentation is for the new OMERO 5.1. version. See the latest OMERO 5.0.x version or the previous versions page to find documentation for the OMERO version you are using if you have not upgraded yet.

Configuration properties glossary

Introduction

The primary form of configuration is via the use of key/value properties, stored in etc/grid/config.xml and read on server startup. Backing up and copying these properties is as easy as copying this file to a new server version.

The etc/omero.properties file of your distribution defines all the default configuration properties used by the server. Changes made to the file are not recognized by the server. Instead, configuration options can be set using the omero config set command:

$ bin/omero config set <parameter> <value>

When supplying a value with spaces or multiple elements, use single quotes. The quotes will not be saved as part of the value (see below).

To remove a configuration option (to return to default values where mentioned), simply omit the value:

$ bin/omero config set <parameter>

These options will be stored in a file: etc/grid/config.xml which you can read for reference. DO NOT edit this file directly.

You can also review all your settings by using:

$ bin/omero config get

which should return values without quotation marks.

A final useful option of omero config edit is:

$ bin/omero config edit

which will allow for editing the configuration in a system-default text editor.

Note

Please use the escape sequence \" for nesting double quotes (e.g. "[\"foo\", \"bar\"]") or wrap with ' (e.g. '["foo", "bar"]').

Examples of doing this are on the main Unix and Windows pages, as well as the LDAP installation page.

Client

omero.client.scripts_to_ignore

Server-side scripts used in IScript service Clients shouldn’t display.

Default: /omero/figure_scripts/Movie_Figure.py, /omero/figure_scripts/Split_View_Figure.py, /omero/figure_scripts/Thumbnail_Figure.py, /omero/figure_scripts/ROI_Split_Figure.py, /omero/export_scripts/Make_Movie.py, /omero/setup_scripts/FLIM_initialise.py, /omero/import_scripts/Populate_ROI.py

omero.client.ui.menu.dropdown.colleagues

Client dropdown menu colleagues label.

Default: Members

omero.client.ui.menu.dropdown.colleagues.enabled

Flag to show/hide colleagues

Default: true

omero.client.ui.menu.dropdown.everyone

Client dropdown menu all users label.

Default: All Members

omero.client.ui.menu.dropdown.everyone.enabled

Flag to show/hide all users.

Default: true

omero.client.ui.menu.dropdown.leaders

Client dropdown menu leader label.

Default: Owners

omero.client.ui.menu.dropdown.leaders.enabled

Default: true

omero.client.ui.tree.orphans.description

Description of the “Orphaned images” container.

Default: This is a virtual container with orphaned images. These images are not linked anywhere. Just drag them to the selected container.

omero.client.ui.tree.orphans.name

Name of the “Orphaned images” container located in client tree data manager.

Default: Orphaned images

Core

omero.data.dir

Default: /OMERO/

omero.db.authority

Default: export.openmicroscopy.org

omero.db.host

Default: localhost

omero.db.name

Default: omero

omero.db.pass

Default: omero

omero.db.patch

Default: 1

omero.db.poolsize

Sets the number of connections to PostgreSQL which will be used by OMERO. Your database installation will need to be configured to accept at least as many, preferably more, connections as this value.

Default: 10

omero.db.prepared_statement_cache_size

Default: 10

omero.db.profile

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

Default: psql

omero.db.statistics

Whether JMX statistics are collected for DB usage (by Hibernate, etc)

Default: true

omero.db.user

Default: omero

omero.db.version

Default: OMERO5.1

FS

omero.checksum.supported

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
  • File-Size-64

In negotiation with clients, this list is interpreted as being in descending order of preference.

Default: SHA1-160, MD5-128, Murmur3-128, Murmur3-32, CRC-32, Adler-32, File-Size-64

omero.fs.repo.path

Template for FS managed repository paths. Allowable elements are:

%user%         bob
%userId%       4
%group%        bobLab
%groupId%      3
%year%         2011
%month%        01
%monthname%    January
%day%          01
%time%         15-13-54.014
%institution%  University of Dundee
%hash%         0D2D8DB7
%increment%    14
%subdirs%      023/613
%session%      c3fdd5d8-831a-40ff-80f2-0ba5baef448a
%sessionId%    592
%perms%        rw----
/              path separator
//             end of root-owned directories

These are described further at FS configuration options

The path must be unique per fileset to prevent upload conflicts, which is why %time% includes milliseconds.

A // may be used as a path separator: the directories preceding it are created with root ownership, the remainder are the user’s. At least one user-owned directory must be included in the path.

The template path is created below omero.managed.dir, e.g. /OMERO/ManagedRepository/<omero.fs.repo.path>/

Default: %user%_%userId%//%year%-%month%/%day%/%time%

omero.fs.repo.path_rules

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
  • local required
  • local 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. “local” means “Windows” or “UNIX” depending on the local platform, the latter being applied for Linux and Mac OS X.

Default: Windows required, UNIX required

omero.managed.dir

Default: ${omero.data.dir}/ManagedRepository

Graphs

omero.graphs.wrap

Whether to use the new Chgrp, Chown, Delete implementations. Available only for OMERO 5.1: from OMERO 5.2 the new implementations must be used.

Default: true

Grid

omero.cluster.read_only

Default: false

omero.cluster.redirector

Default: nullRedirector

omero.grid.registry_timeout

registry_timeout is the milliseconds which the registry and other services will wait on remote services to respond.

Default: 5000

Ice

Ice.IPv6

Disable IPv6 by setting to 0. Only needed in certain situations.

Default: 1

JVM

omero.jvmcfg.append

Contains other parameters which should be passed to the JVM. The value of “append” is treated as if it were on the command-line and so will be separated on whitespace. For example, ‘-XX:-PrintGC -XX:+UseCompressedOops’ would results in two new arguments.

Default: [empty]

omero.jvmcfg.heap_dump

Toggles on or off heap dumps on OOMs. Default is “off”. The special value “tmp” will create the heap dumps in your temp directory.

Default: [empty]

omero.jvmcfg.heap_size

Explicit value for the -Xmx argument, e.g. “1g”

Default: [empty]

omero.jvmcfg.max_system_memory

Suggestion for strategies as to the maximum memory that they will use for calculating JVM settings (MB).

Default: 48000

omero.jvmcfg.min_system_memory

Suggestion for strategies as to the minimum memory that they will use for calculating JVM settings (MB).

Default: 3414

omero.jvmcfg.percent

Used only by the percent strategy. An integer between 0 and 100 which is the percent of active memory that will be used by the service.

Default: [empty]

omero.jvmcfg.perm_gen

Explicit value for the MaxPermSize argument to the JVM, e.g. “500M”

Default: [empty]

omero.jvmcfg.strategy

Memory strategy which will be used by default. Options include: percent, manual

Default: percent

omero.jvmcfg.system_memory

Manual override of the total system memory that OMERO will think is present on the local OS (MB). If unset, an attempt will be made to detect the actual amount: first by using the Python library psutil and if that is not installed, by running a Java tool. If neither works, 4.0GB is assumed.

Default: [empty]

LDAP

omero.ldap.base

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)

Default: ou=example, o=com

omero.ldap.config

Enable or disable LDAP (true or false).

Default: false

omero.ldap.group_filter

Default: (objectClass=groupOfNames)

omero.ldap.group_mapping

Default: name=cn

omero.ldap.new_user_group

Default: default

omero.ldap.password

LDAP server bind password (if required; can be empty)

Default: [empty]

omero.ldap.referral

Available referral options are: “ignore”, “follow”, or “throw” as per the JNDI referral documentation.

Default: ignore

omero.ldap.sync_on_login

Whether or not values from LDAP will be synchronized 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.

Default: false

omero.ldap.urls

Set the URL of the LDAP server. A SSL URL for this property would be of the form: ldaps://ldap.example.com:636

Default: ldap://localhost:389

omero.ldap.user_filter

Default: (objectClass=person)

omero.ldap.user_mapping

Default: omeName=cn, firstName=givenName, lastName=sn, email=mail

omero.ldap.username

LDAP server bind DN (if required; can be empty)

Default: [empty]

Mail

omero.mail.bean

Mail sender properties

Default: defaultMailSender

omero.mail.config

Enable or disable mail sender (true or false).

Default: false

omero.mail.from

the email address used for the “from” field

Default: omero@${omero.mail.host}

omero.mail.host

the hostname of smtp server

Default: localhost

omero.mail.password

the password to connect to the smtp server (if required; can be empty)

Default: [empty]

omero.mail.port

the port of smtp server

Default: 25

omero.mail.smtp.auth

see javax.mail.Session properties

Default: false

omero.mail.smtp.connectiontimeout

Default: 60000

omero.mail.smtp.debug

Default: false

omero.mail.smtp.socketFactory.class

Default: javax.net.SocketFactory

omero.mail.smtp.socketFactory.fallback

Default: false

omero.mail.smtp.socketFactory.port

Default: ${omero.mail.port}

omero.mail.smtp.starttls.enable

Default: false

omero.mail.smtp.timeout

Default: 60000

omero.mail.transport.protocol

other smtp parameters; see org.springframework.mail.javamail.JavaMailSenderImpl

Default: smtp

omero.mail.username

the user name to connect to the smtp server (if required; can be empty)

Default: [empty]

Metrics

omero.metrics.bean

Which bean to use: nullMetrics does nothing defaultMetrics uses the properties defined below

Default: defaultMetrics

omero.metrics.graphite

Address for Metrics to send server data

Default: [empty]

omero.metrics.slf4j_minutes

Number of minutes to periodically print to slf4j 0 or lower disables the printout.

Default: 60

Performance

omero.sessions.maximum

Default: 0

omero.sessions.sync_force

Default: 1800000

omero.sessions.sync_interval

Default: 120000

omero.sessions.timeout

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

Default: 600000

omero.threads.cancel_timeout

Default: 5000

omero.threads.idle_timeout

Default: 5000

omero.threads.max_threads

Default: 50

omero.threads.min_threads

Default: 5

omero.throttling.method_time.error

Default: 20000

omero.throttling.method_time.error.indexer

Value for the indexer is extended to 1 day

Default: 86400000

omero.throttling.method_time.warn

Default: 5000

omero.throttling.method_time.warn.indexer

Value for the indexer is extended to 1 hour

Default: 3600000

omero.throttling.objects_read_interval

Default: 1000

omero.throttling.objects_written_interval

Default: 1000

omero.throttling.servants_per_session

Default: 10000

Pixeldata

omero.pixeldata.backoff

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.

Default: ome.io.nio.SimpleBackOff

omero.pixeldata.batch

Number of instances indexed per indexing. (Ignored by pixelDataEventLogQueue)

Default: 50

omero.pixeldata.cron

Polling frequency of the pixeldata processing. Set empty to disable pixeldata processing.

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 the CronTrigger Tutorial.

Default: */4 * * * * ?

omero.pixeldata.dispose

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.

Default: true

omero.pixeldata.event_log_loader

EventLogLoader that will be used for loading EventLogs for the action “PIXELDATA”. Choices include: pixelDataEventLogQueue and the older pixelDataPersistentEventLogLoader

Default: pixelDataEventLogQueue

omero.pixeldata.max_plane_height

Default: 3192

omero.pixeldata.max_plane_width

Default: 3192

omero.pixeldata.memoizer_wait

Maximum time in milliseconds that file parsing can take without the parsed metadata being cached to BioFormatsCache.

Default: 0

omero.pixeldata.repetitions

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

(Ignored by pixelDataEventLogQueue; uses threads instead)

Default: 1

omero.pixeldata.threads

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.

Default: 2

omero.pixeldata.tile_height

Default: 256

omero.pixeldata.tile_sizes_bean

Default sizes for tiles are provided by a ome.io.nio.TileSizes implementation. By default the bean (“configuredTileSizes”) uses the properties provided here.

Default: configuredTileSizes

omero.pixeldata.tile_width

Default: 256

Policy

omero.policy.bean

Instance of the PolicyService interface which will be responsible for checking certain server actions made by a user.

Default: defaultPolicyService

omero.policy.binary_access

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.

Default: +read, +write, +image

Scripts

omero.launcher.jython

Default: jython

omero.launcher.matlab

Default: matlab

omero.launcher.python

No value implies use sys.executable

Default: [empty]

omero.process.jython

Default: omero.processor.ProcessI

omero.process.matlab

Default: omero.processor.MATLABProcessI

omero.process.python

Default: omero.processor.ProcessI

omero.scripts.timeout

Default: 3600000

Security

omero.security.chmod_strategy

Default: groupChmodStrategy

omero.security.filter.bitand

Default: (int8and(permissions, %s) = %s)

omero.security.keyStore

A keystore is a database of private keys and their associated X.509 certificate chains authenticating the corresponding public keys. A keystore is mostly needed if you are doing client-side certificates for authentication against your LDAP server.

Default: [empty]

omero.security.keyStorePassword

Sets the password of the keystore

Default: [empty]

omero.security.login_failure_throttle_count

Default: 1

omero.security.login_failure_throttle_time

Default: 3000

omero.security.password_provider

Implementation of PasswordProvider that will be used to authenticate users. Typically, a chanined password provider will be used so that if one form of authentication (e.g. LDAP) does not work, other attempts will be made.

Default: chainedPasswordProvider

omero.security.password_required

Controls whether the server will allow creation of user accounts with an empty password. If set to true (default, strict mode), empty passwords are disallowed. This still allows the guest user to interact with the server.

Default: true

omero.security.trustStore

A truststore is a database of trusted entities and their associated X.509 certificate chains authenticating the corresponding public keys. The truststore contains the Certificate Authority (CA) certificates and the certificate(s) of the other party to which this entity intends to send encrypted (confidential) data. This file must contain the public key certificates of the CA and the client’s public key certificate.

Default: [empty]

omero.security.trustStorePassword

Sets the password of the truststore

Default: [empty]

Web

omero.web.admins

A list of people who get code error notifications whenever the application identify broken link or raises an unhandled exception that results in an internal server error. This gives the administrators immediate notification of any errors, see OMERO.mail. Example:'[["Full Name", "email address"]]'.

Default: []

omero.web.application_server

OMERO.web is configured to use FastCGI TCP by default. If you are using a non-standard web server configuration you may wish to change this before generating your web server configuration. Available options “fastcgi” / “fastcgi-tcp”

Default: fastcgi-tcp

omero.web.application_server.host

Upstream application host

Default: 127.0.0.1

omero.web.application_server.max_requests

Default: 400

omero.web.application_server.port

Upstream application port

Default: 4080

omero.web.apps

Add additional Django applications. For example, see Creating an app

Default: []

omero.web.caches

OMERO.web offers alternative session backends to automatically delete stale data using the cache session store backend, see Django cached session documentation for more details.

Default: {“default”: {“BACKEND”: “django.core.cache.backends.dummy.DummyCache”}}

omero.web.databases

Default: {}

omero.web.debug

A boolean that turns on/off debug mode.

Default: false

omero.web.index_template

Define template used as an index page http://your_host/omero/.If None user is automaticaly redirected to the login page.For example use ‘webstart/start.html’.

Default: None

omero.web.logdir

A path to the custom log directory.

Default: /home/omero/OMERO.server/var/log

omero.web.login_redirect

Redirect to the givin location after loging in. It only support arguments for Django reverse function. For example: '{"redirect": ["webindex"], "viewname": "load_template", "args":["userdata"], "query_string": "experimenter=-1"}'

Default: {}

omero.web.login_view

Default: weblogin

omero.web.open_astex_max_side

Default: 400

omero.web.open_astex_max_voxels

Default: 27000000

omero.web.open_astex_min_side

Default: 20

omero.web.page_size

Number of images displayed within a dataset or ‘orphaned’ container to prevent from loading them all at once.

Default: 200

omero.web.ping_interval

description

Default: 60000

omero.web.pipeline_css_compressor

Compressor class to be applied to CSS files. If empty or None, CSS files won’t be compressed.

Default: None

omero.web.pipeline_js_compressor

Compressor class to be applied to JavaScript files. If empty or None, JavaScript files won’t be compressed.

Default: None

omero.web.pipeline_staticfile_storage

The file storage engine to use when collecting static files with the collectstatic management command. See the documentation for more details.

Default: pipeline.storage.PipelineStorage

omero.web.prefix

Used as the value of the SCRIPT_NAME environment variable in any HTTP request.

Default: None

omero.web.public.cache.enabled

Default: false

omero.web.public.cache.key

Default: omero.web.public.cache.key

omero.web.public.cache.timeout

Default: 86400

omero.web.public.enabled

Enable and disable the OMERO.web public user functionality.

Default: false

omero.web.public.password

Password to use during authentication.

Default: None

omero.web.public.server_id

Server to authenticate against.

Default: 1

omero.web.public.url_filter

Set a URL filter for which the OMERO.web public user is allowed to navigate. The idea is that you can create the public pages yourself (see OMERO.web framework since we do not provide public pages.

Default: ^/(?!webadmin)

omero.web.public.user

Username to use during authentication.

Default: None

omero.web.server_list

A list of servers the Web client can connect to.

Default: [[“localhost”, 4064, “omero”]]

omero.web.session_engine

Controls where Django stores session data. See Configuring the session engine for more details.

Default: omeroweb.filesessionstore

omero.web.session_expire_at_browser_close

A boolean that determines whether to expire the session when the user closes their browser. See Django Browser-length sessions vs. persistent sessions documentation for more details.

Default: true

omero.web.static_url

URL to use when referring to static files. Example: '/static/' or 'http://static.example.com/'. Used as the base path for asset definitions (the Media class) and the staticfiles app. It must end in a slash if set to a non-empty value.

Default: /static/

omero.web.staticfile_dirs

Defines the additional locations the staticfiles app will traverse if the FileSystemFinder finder is enabled, e.g. if you use the collectstatic or findstatic management command or use the static file serving view.

Default: []

omero.web.template_dirs

List of locations of the template source files, in search order. Note that these paths should use Unix-style forward slashes, even on Windows.

Default: []

omero.web.ui.center_plugins

Add plugins to the center panels. Plugins are ['Channel overlay', 'webtest/webclient_plugins/center_plugin.overlay.js.html', 'channel_overlay_panel']. The javascript loads data into $('#div_id').

Default: []

omero.web.ui.right_plugins

Add plugins to the right-hand panel. Plugins are ['Label', 'include.js', 'div_id']. The javascript loads data into $('#div_id').

Default: [[“Acquisition”, “webclient/data/includes/right_plugin.acquisition.js.html”, “metadata_tab”],[“Preview”, “webclient/data/includes/right_plugin.preview.js.html”, “preview_tab”]]

omero.web.viewer.initial_zoom_level

Configuration options for the viewer. -1: zoom in fully, 0: zoom out fully, unset: zoom to fit window

Default: None

omero.web.webgateway_cache

Default: None