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Configuration properties glossary

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, the omero config command is used to change those properties that you would like to customize.

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

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: 0
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: OMERO5.0

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

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.

Default: Windows required, UNIX required

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

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 binard 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 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.

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]

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.

Default: 50

omero.pixeldata.cron

Polling frequency of the pixeldata processing. Set empty to disable pixelsdata 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 informatin, 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: false

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.

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

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.resetpassword.bean
Default: defaultMailSender
omero.resetpassword.config
Default: false
omero.resetpassword.from
Default: ADDRESS@domain
omero.resetpassword.host
Default: smtp.domain
omero.resetpassword.mail.debug
Default: false
omero.resetpassword.mail.smtp.auth
Default: false
omero.resetpassword.mail.smtp.socketFactory.class
Default: javax.net.SocketFactory
omero.resetpassword.mail.smtp.socketFactory.fallback
Default: false
omero.resetpassword.mail.smtp.socketFactory.port
Default: 25
omero.resetpassword.mail.smtp.starttls.enable
Default: false
omero.resetpassword.mail.smtp.timeout
Default: 25000
omero.resetpassword.mail.transport.protocol
Default: smtp
omero.resetpassword.password
Default: [empty]
omero.resetpassword.port
Default: 25
omero.resetpassword.username
Default: [empty]
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
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]