.. This file is auto-generated from omero.properties. DO NOT EDIT IT Configuration properties glossary ================================= The primary form of configuration is via the use of key/value properties, stored in :file:`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 :source:`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 :omerocmd:`config` command is used to change those properties that you would like to customize. Examples of doing this are on the main :doc:`Unix ` and :doc:`Windows ` pages, as well as the :doc:`LDAP installation ` page. .. _core_configuration: Core ---- .. glossary:: 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_configuration: FS -- .. glossary:: 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 :doc:`fs-upload-configuration` 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 :term:`omero.managed.dir`, e.g. /OMERO/ManagedRepository// 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 :term:`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_configuration: Grid ---- .. glossary:: 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_configuration: Ice --- .. glossary:: Ice.IPv6 Disable IPv6 by setting to 0. Only needed in certain situations. Default: `1` .. _jvm_configuration: JVM --- .. glossary:: 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_configuration: LDAP ---- .. glossary:: 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_configuration: Metrics ------- .. glossary:: 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_configuration: Performance ----------- .. glossary:: 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_configuration: Pixeldata --------- .. glossary:: 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| replace:: 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`_. .. _CronTrigger Tutorial: http://quartz-scheduler.org/documentation/quartz-1.x/tutorials/crontrigger |cron| 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_configuration: Scripts ------- .. glossary:: 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` .. _search_configuration: Search ------ .. glossary:: omero.search.analyzer Analyzer used both index and to parse queries Default: `ome.services.fulltext.FullTextAnalyzer` omero.search.batch Size of the batches to process events per indexing. Larger batches can speed up indexing, but at the cost of memory. Default: `5000` omero.search.bridges Extra bridge classes, comma-separated, to be invoked on each indexing. Bridges are used to parse more information out of the data. Default: `[empty]` omero.search.cron Polling frequency of the indexing. Set empty to disable search indexing. |cron| Default: `*/2 * * * * ?` omero.search.event_log_loader Default: `eventLogQueue` omero.search.excludes 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. Default: `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` omero.search.include_actions EventLog.action values which will be indexed. Unless custom code is generating other action types, this property should not need to be modified. Default: `INSERT,UPDATE,REINDEX,DELETE` omero.search.include_types 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. Default: `ome.model.core.Image,ome.model.containers.Project,ome.model.containers.Dataset,ome.model.screen.Plate,ome.model.screen.Screen` omero.search.locking_strategy Default: `native` omero.search.max_file_size 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`). Default: `131072000` omero.search.max_partition_size 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. Default: `1000000` omero.search.maxclause Maximum number of OR-clauses to which a single search can expand Default: `4096` omero.search.merge_factor Default: `25` omero.search.ram_buffer_size Default: `64` omero.search.repetitions 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) Default: `1` omero.search.reporting_loops Periodically the completion percentage will be printed. The calculation can be expensive and so is not done frequently. Default: `100` .. _security_configuration: Security -------- .. glossary:: 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]`