Configuration properties by module
AS Modules
Database Configuration (Required)
Key |
Example Value |
Short Explanation |
|---|---|---|
database.active-connections-log-interval |
3600 |
Log interval (in seconds) between two regular log entries of the number of active database |
database.admin-password |
||
database.admin-user |
postgres |
Superuser of the database. |
database-instance |
DEFAULT |
The database instance local unique identifier. |
database.kind |
prod |
|
database.max-active-connections |
20 |
Max. number of active database connections. |
database.max-idle-connections |
20 |
Max. number of idle database connections to keep open. |
database.owner |
openbis |
User who owns the database. Default: Operating system user running the server. |
database.owner-password |
||
database.url-host-part |
localhost |
The host and optionally port. |
Session Configuration (Required)
Key |
Example Value |
Short Explanation |
|---|---|---|
max-number-of-sessions-per-user |
5 |
The maximum number of sessions a single user is allowed to have open |
personal-access-tokens-enabled |
true |
Enable personal access tokens |
personal-access-tokens-file-path |
${root-dir}/personal-access-tokens.json |
|
personal-access-tokens-max-validity-period |
2592000 |
Validity of personal access tokens |
personal-access-tokens-validity-warning-period |
432000 |
|
session-workspace-root-dir |
${storeroot-dir}/sessionWorkspace |
|
session-timeout |
720 |
The time after which an inactive session is expired by the service (in minutes). |
session-timeout-no-login |
10 |
Session time (in minutes) in case of presents of file etc/nologin.html. Should be < 30. |
users-with-unrestricted-number-of-sessions |
etlserver |
Specify user(s) allowed to have an unrestriced amount of sessions. This is typically only useful for the internal etlserver user (the user contacting the openBIS Application Server) |
Mail server Configuration (Optional)
Key |
example Value |
Short Explanation |
|---|---|---|
mail.from |
openbis@openbis-eln-weis.ethz.ch |
|
mail.smtp.host |
localhost |
|
mail.smtp.password |
||
mail.smtp.user |
Exports Configuration (Optional)
Key |
Example Value |
Short Explanation |
|---|---|---|
download-url |
https://localhost |
The base URL for Web client access. |
export.data-limit |
10737418240 |
Export data limit in bytes |
Imports Configuration (Optional)
Key |
Example Value |
Short Explanation |
|---|---|---|
xls-import.version-data-file |
../../../xls-import-version-info.json |
Path to the file which stores version information of master data imported from Excel sheets. |
Authentication Configuration (Required)
Key |
Example Value |
Short Explanation |
|---|---|---|
allow-missing-user-creation |
false |
When a new person is created in the database the authentication service is asked by default whether this person is known by the authentication service |
authentication-service |
file-authentication-service |
Authentication configuration - can be ‘file-authentication-service’, ‘ldap-authentication-service’, or ‘file-ldap-authentication-service’ |
authentication-service.switch-aai.label |
Single Sign On Login Service |
Label of the single sign-on (shibboleth) login service provider |
authentication-service.switch-aai.link |
https://${host}/Shibboleth.sso/Login?target=https://${host}/shibboleth?redirect-url=${current-url} |
URL to be used for authenticating via the shibboleth login service provider |
ldap.server.url |
The space-separated URLs of the LDAP servers |
|
ldap.security.principal.distinguished.name |
The distinguished name of the security principal |
|
ldap.security.principal.password |
||
ldap.security.protocol |
||
ldap.security.authentication-method |
||
ldap.referral |
||
ldap.searchBase |
||
ldap.attributenames.user.id |
||
ldap.attributenames.email |
||
ldap.attributenames.first.name |
||
ldap.attributenames.last.name |
||
ldap.queryEmailForAliases |
||
ldap.queryTemplate |
||
ldap.maxRetries |
||
ldap.timeout |
||
ldap.timeToWaitAfterFailure |
||
user-for-anonymous-login |
Login of the existing user whose settings will be used for anonymous login |
|
single-sign-on.enabled |
false |
Used to switch on or off single sign-on authentication |
Hibernate Search Configuration (Optional)
Key |
Example Value |
Short Explanation |
|---|---|---|
hibernate.search.batch-size |
1000 |
|
hibernate.search.index-base |
./indices |
|
hibernate.search.index-mode |
SKIP_IF_MARKER_FOUND |
|
hibernate.search.maxResults |
100000 |
|
hibernate.search.worker.execution |
async |
AutoArchiver Configuration (Optional)
Key |
Example Value |
Short Explanation |
|---|---|---|
|
ch.systemsx.cisd.etlserver.plugins.AgeArchiveCandidateDiscoverer |
Archive candidate discoverer class specification |
|
ch.systemsx.cisd.etlserver.plugins.AutoArchiverTask |
Auto archiver task class specificication |
|
Data set type to be archived by this AutoArchiver |
|
|
Time interval specifying by what interval the AutoArchiver should check if new datasets matching the autoarchiving criteria are available for archiving |
|
|
Minimum age that datasets need to have in order to be archived by the AutoArchiver |
|
|
ch.systemsx.cisd.etlserver.plugins.GroupingPolicy |
Policy class specification |
|
Keys by which to group datasets for archiving |
|
|
200000000000 |
Maximum size of container file (tar file) to be created by the AutoArchiver |
|
10000000000 |
Minimum size of container file (tar file) to be created by the AutoArchiver |
|
true |
Remove datasets from store after the archiving is complete (true) or not (false) |
Usage Reporting (Optional)
Key |
Example Value |
Short Explanation |
|---|---|---|
usage-reporting.class |
ch.systemsx.cisd.openbis.generic.server.task.UsageReportingTask |
|
usage-reporting.configuration-file-path |
${root-dir}/user-management-maintenance-config.json |
|
usage-reporting.email-addresses |
||
usage-reporting.interval |
60 min |
|
usage-reporting.path-to-save-report |
${root-dir} |
|
usage-reporting.report-name-prefix |
||
usage-reporting.run-schedule |
1. 00:15 |
|
usage-reporting.spaces-to-be-ignored |
||
usage-reporting.start |
00:15 |
|
usage-reporting.title-name-prefix |
||
usage-reporting.user-reporting-type |
ALL |
User Management (Optional, Required for multi-group setups)
Key |
Example Value |
Short Explanation |
|---|---|---|
user-management.audit-log-file-path |
/var/log/user-management-audit.log |
Path to user-managment audit log file |
user-management.class |
ch.systemsx.cisd.openbis.generic.server.task.UserManagementMaintenanceTask |
|
user-management.configuration-file-path |
${root-dir}/user-management-maintenance-config.json |
|
user-management.deactivate-unknown-users |
false |
Deactivate users unkown to the authentication backend (true) or not (false) |
user-management.interval |
1 h |
Time interval by how often the user-management task should be invoked |
user-management.ldap-group-query-template |
||
user-management.shares-mapping-file-path |
${root-dir}/shares-mapping.txt |
Path to shares-mapping file. Must match the value of post-registration.eager-shuffling.share-finder.mapping-file |
user-management.start |
02:00 |
Time (%H:%M) by when to start the user-management |
Miscellaneous Configuration (Optional)
Key |
Example Value |
Short Explanation |
|---|---|---|
authorization-component-factory |
active-authorization |
Internal - do not change |
authorization.project-level.enabled |
true |
|
authorization.project-level.users |
.* |
|
create-continuous-sample-codes |
true |
|
data-set-types-with-no-experiment-needed |
||
entity-history.enabled |
true |
Enables/disables history of deleted entities. Default value is ‘true’, keeping entity history has a performance overhead on updates. On certain scenarios you might not want it. |
jython-version |
2.7 |
Internal - do not change |
maintenance-plugins |
Comma-separated list of maintenance plugins to be configured for the AS |
|
project-samples-enabled |
true |
|
script-folder |
. |
Internal - do not change |
web-client-configuration-file |
||
trusted-cross-origin-domains |
* |
V3 API Configuration (Optional)
Key |
Example Value |
Short Explanation |
|---|---|---|
api.v3.fast-download.maximum-number-of-allowed-streams |
50 |
The maximum number of allowed download streams |
api.v3.operation-execution.availability-time.default |
||
api.v3.operation-execution.availability-time.max |
||
api.v3.operation-execution.availability-time.summary.default |
||
api.v3.operation-execution.availability-time.summary.max |
||
api.v3.operation-execution.availability-time.details.default |
||
api.v3.operation-execution.availability-time.details.max |
||
api.v3.operation-execution.availability-update.mark-timeout-pending-task.name |
||
api.v3.operation-execution.availability-update.mark-timeout-pending-task.interval |
||
api.v3.operation-execution.availability-update.mark-timed-out-or-deleted-task.name |
||
api.v3.operation-execution.availability-update.mark-timed-out-or-deleted-task.interval |
||
api.v3.operation-execution.cache.capacity |
10240 |
|
api.v3.operation-execution.cache.class |
ch.ethz.sis.openbis.generic.server.asapi.v3.executor.common.search.cache.FileCache |
|
api.v3.operation-execution.cache.clearance-task-name |
cache-clearance-task |
|
api.v3.operation-execution.cache.directory |
targets/sessionWorkspace/cache |
|
api.v3.operation-execution.cache.timeout |
3600 |
|
api.v3.operation-execution.cache.timeout-check-interval |
300 |
|
api.v3.operation-execution.progress.thread-name |
||
api.v3.operation-execution.progress.interval |
||
api.v3.operation-execution.state-update.mark-failed-after-server-restart-task.name |
||
api.v3.operation-execution.store.path |
||
api.v3.operation-execution.thread-pool.name |
||
api.v3.operation-execution.thread-pool.core-size |
||
api.v3.operation-execution.thread-pool.max-size |
||
api.v3.operation-execution.thread-pool.keep-alive-time |
||
api.v3.transaction.coordinator-key |
||
api.v3.transaction.enabled |
||
api.v3.transaction.finish-transactions-interval |
||
api.v3.transaction.interactive-session-key |
||
api.v3.transaction.participant.application-server.timeout |
||
api.v3.transaction.participant.application-server.url |
||
api.v3.transaction.participant.afs-server.timeout |
||
api.v3.transaction.participant.afs-server.url |
||
api.v3.transaction.transaction-count-limit |
||
api.v3.transaction.transaction-log-folder-path |
||
api.v3.transaction.transaction-timeout |
DSS Modules
Core Configuration (Required)
Key |
Example Value |
Short Explanation |
|---|---|---|
cache-workspace-folder |
${root-dir}/dss-cache |
Cache for data set files from other Data Store Servers |
check-interval |
5 |
The check interval (in seconds) |
commandqueue-dir |
/home/openbis/run/datastore_commandqueue |
The directory where the command queue file is located |
data-set-command-queue-mapping |
Comma-separated list of definitions of additional queues for processing processing plugins. |
|
data-store-server-code |
DSS1 |
Unique code of this Data Store Server. |
download-url |
${host-address}:${port} |
The base URL for Web client access to the data store server. |
experiment-name-property-code |
name |
|
highwater-mark |
-1 |
Data Set Registration Halt |
host-address |
http://localhost |
host name of the machine on which the datastore server is running |
incoming-root-dir |
${root-dir} |
|
jython-version |
2.7 |
|
keystore.key-password |
changeit |
Key password of the keystore |
keystore.password |
changeit |
Password of the keystore |
keystore.path |
etc/openBIS.keystore |
Path to the keystore |
minimum-time-to-keep-streams-in-sec |
20 |
The minimum time (in seconds) of availability of the data stream since moment when user requested for the data stream url. |
notify-successful-registration |
false |
|
password |
The password for the etlserver user who contacts the openBIS server |
|
port |
8081 |
|
quiet-period |
180 |
|
recovery-highwater-mark |
-1 |
Data Set Registration Halt |
root-dir |
/home/openbis/data |
parent directory of the store directory and all the dropboxes |
rsync-options |
–no-p –no-o –no-g –chmod=Du=rwx,Fu=rw –chown=openbis:openbis |
Typical options to disable coping general, owner and group permissions |
sample-name-property-code |
samplename |
|
server-url |
${host-address}:8080 |
The URL of the openBIS server |
session-timeout |
720 |
Session timeout in minutes |
shutdown-timeout |
180 |
The time-out for clean up work in the shutdown sequence (in seconds). |
storeroot-dir |
${root-dir}/store |
The root directory of the data store |
use-ssl |
false |
|
username |
etlserver |
The username to use when contacting the openBIS Application Server (AS) |
Database Configuration (Required)
Key |
Example Value |
Short Explanation |
|---|---|---|
data-sources |
path-info-db |
Data sources |
path-info-db.version-holder-class |
ch.systemsx.cisd.openbis.dss.generic.shared.PathInfoDatabaseVersionHolder |
|
path-info-db.databaseEngineCode |
postgresql |
|
path-info-db.basicDatabaseName |
pathinfo |
|
path-info-db.urlHostPart |
||
path-info-db.databaseKind |
prod |
|
path-info-db.scriptFolder |
${root-dir}/sql |
|
path-info-db.owner |
The owner of the database |
|
path-info-db.password |
Owner password |
|
path-info-db.adminUser |
The administrator user of the database server. |
|
path-info-db.adminPassword |
Administrator password |
Mail server Configuration (Optional)
Key |
Example Value |
Short Explanation |
|---|---|---|
mail.smtp.host |
SMTP properties |
|
mail.from |
||
mail.smtp.user |
||
mail.smtp.password |
Mail server Configuration (Optional)
Key |
Example Value |
Short Explanation |
|---|---|---|
ftp.server.enable |
true |
When set to ‘true’ an internal ftp / sftp server will be started. |
ftp.server.sftp-port |
2222 |
SFTP port |
ftp.resolver-dev-mode |
||
ftp.server.certificate |
Dropbox Configuration (Optional)
Key |
Example Value |
Short Explanation |
|---|---|---|
inputs |
default-dropbox |
|
dss-rpc.put-default |
default-dropbox |
|
default-dropbox.incoming-dir |
${incoming-root-dir}/incoming-default |
|
default-dropbox.incoming-data-completeness-condition |
auto-detection |
|
default-dropbox.program-class |
ch.systemsx.cisd.etlserver.registrator.DefaultDropbox |
|
default-dropbox.storage-processor |
ch.systemsx.cisd.etlserver.DefaultStorageProcessor |
|
default-dropbox.top-level-data-set-handler |
ch.systemsx.cisd.etlserver.registrator.api.v2.JavaTopLevelDataSetHandlerV2 |
|
mail.addresses.dropbox-errors |
Comma-separated list of e-mail addresses that should be notified in case of dropbox errors |
Post Registration Task (Optional)
Key |
Example Value |
Short Explanation |
|---|---|---|
post-registration.class |
ch.systemsx.cisd.etlserver.postregistration.PostRegistrationMaintenanceTask |
Maintenance task for post registration of all paths of a freshly registered data set |
post-registration.interval |
30 |
|
post-registration.cleanup-tasks-folder |
${root-dir}/post-registration/cleanup-tasks |
|
post-registration.last-seen-data-set-file |
${root-dir}/post-registration/last-seen-data-set.txt |
|
post-registration.post-registration-tasks |
pathinfo-feeding |
|
post-registration.pathinfo-feeding.class |
ch.systemsx.cisd.etlserver.path.PathInfoDatabaseFeedingTask |
|
post-registration.pathinfo-feeding.compute-checksum |
true |
|
post-registration.eager-shuffling.class |
ch.systemsx.cisd.etlserver.postregistration.EagerShufflingTask |
|
post-registration.eager-shuffling.share-finder.class |
ch.systemsx.cisd.openbis.dss.generic.shared.MappingBasedShareFinder |
|
post-registration.eager-shuffling.share-finder.mapping-file |
${root-dir}/shares-mapping.txt |
Processing Plugins (Optional)
Key |
Example Value |
Short Explanation |
|---|---|---|
processing-plugins |
path-info-db-consistency-check |
Comma separated names of processing plugins. |
path-info-db-consistency-check.label |
Path Info DB consistency check |
Processing task that checks the consistency between the data store and the meta information stored in the PathInfoDB. |
path-info-db-consistency-check.dataset-types |
.* |
|
path-info-db-consistency-check.class |
ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.DataSetAndPathInfoDBConsistencyCheckProcessingPlugin |
Maintenance Plugins (Optional)
Key |
Example Value |
Short Explanation |
|---|---|---|
maintenance-plugins |
post-registration, path-info-deletion, data-set-and-path-info-db-consistency-check-task, fill-unknown-data-set-size-in-openbis-db-from-path-info-db, data-set-archiver-orphan-finder-task |
Comma separated names of maintenance plugins. |
path-info-deletion.class |
ch.systemsx.cisd.etlserver.plugins.DeleteFromExternalDBMaintenanceTask |
Maintenance task for deleting entries from pathinfo database |
path-info-deletion.interval |
120 |
|
path-info-deletion.data-source |
path-info-db |
|
path-info-deletion.data-set-table-name |
data_sets |
|
path-info-deletion.data-set-perm-id |
CODE |
|
data-set-and-path-info-db-consistency-check-task.checking-time-interval |
36500 days |
|
data-set-and-path-info-db-consistency-check-task.class |
ch.systemsx.cisd.etlserver.path.DataSetAndPathInfoDBConsistencyCheckTask |
|
data-set-and-path-info-db-consistency-check-task.continuing-time-point |
22:00 |
|
data-set-and-path-info-db-consistency-check-task.pausing-time-point |
09:00 |
|
data-set-and-path-info-db-consistency-check-task.run-schedule |
cron: 0 0 22 5 * * |
|
fill-unknown-data-set-size-in-openbis-db-from-path-info-db.class |
ch.systemsx.cisd.etlserver.plugins.FillUnknownDataSetSizeInOpenbisDBFromPathInfoDBMaintenanceTask |
|
fill-unknown-data-set-size-in-openbis-db-from-path-info-db.data-set-chunk-size |
1000 |
|
fill-unknown-data-set-size-in-openbis-db-from-path-info-db.run-schedule |
cron: 0 0 22 * * SUN |
|
fill-unknown-data-set-size-in-openbis-db-from-path-info-db.time-limit |
3 hours |
|
data-set-archiver-orphan-finder-task.class |
ch.systemsx.cisd.etlserver.plugins.DataSetArchiverOrphanFinderTask |
|
data-set-archiver-orphan-finder-task.run-schedule |
cron: 0 15 1 * * * |
|
data-set-archiver-orphan-finder-task.email-addresses |
Archiver Configuration (Optional)
Key |
Example Value |
Short Explanation |
|---|---|---|
archiver.batch-size-in-bytes |
1520000000000 |
Size of batches of datasets to be archived. Should be marginally higher than archiver.maximum_container_size_in_bytes |
archiver.class |
ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.archiver.MultiDataSetArchiver |
Archiver class specification |
archiver.cleaner.deletion-requests-dir |
${storeroot-dir} |
Directory pointing to the store from which deletions shall be performed after an archiving request has succeeded |
archiver.cleaner.email-address |
Email address that archiver deletion failures should be sent to |
|
archiver.cleaner.email-from-address |
Email address used as the sender address in emails notifying about failed deletions |
|
archiver.cleaner.email-subject |
MultiDatasetArchiver: Deletion failure |
Email subject to be used in emails informing about deletion failures |
archiver.cleaner.email-template |
The following files could not be deleted:\n${file-list} |
Template for the email body to be sent in case of deletion failures |
archiver.cleaner.file-path-prefixes-for-async-deletion |
Comma-separated list of paths to be used for asynchronous deletions on the remote storage volume. This should match the list of mountpoints specified in archiver.final-destination and archiver.replicated-destination |
|
archiver.data-source |
multi-dataset-archiver-db |
The name of the database to be used by the archiver |
archiver.database.kind |
prod |
|
archiver.dataset-unarchiving-highwater-mark |
Highwater mark for unarchiving |
|
archiver.final-destination |
Path to the mounted storage volume representing the final (primary) location of the archiver backend (e.g., a mounted tape drive) |
|
archiver.finalizer-max-waiting-time |
14 d |
Maximum amount of time that the archiver is waiting for an archiving job to complete (both the primary and replica destinations contain a validated copy of the archived data) |
archiver.finalizer-polling-time |
120 min |
Time period the archiver waits after the finalization of the data transfer to the primary destination before checking for t-flags and/or running sanity checks |
archiver.finalizer-sanity-check |
true |
Perform a sanity check after the data to be archived has been copied to the primary destination |
archiver.finalizer-wait-for-t-flag |
true |
Wait for the container file (.tar) in the final destination to be flagged with a “t” (used for tape backends that set this flag to indicate that the copying of the data to the actual tape is complete) |
archiver.hdf5-files-in-data-set |
false |
Specify whether any of the datasets to be archived may contain HDF5-formatted files. If this is not set, proper archiving of those files will fail. |
archiver.maximum-container-size-in-bytes |
1500000000000 |
Maximum size of container files (tar files) to be created by the archiver |
archiver.maximum-unarchiving-capacity-in-megabytes |
2000000 |
Size of the scratch volume (in MB) to be used for unarchiving data from the archive system |
archiver.minimum-container-size-in-bytes |
10000000000 |
Minimum size of container files (tar files) to be created by the archiver |
archiver.pause-file-polling-time |
10 min |
Time used to polling (querying) the file specified in archiver.pause-file |
archiver.pause-file |
${root-dir}/pause-archiving |
Pause archiving until this file has been removed |
archiver.replicated-destination |
Path to the mounted storage volume representing the secondary (replica) location of the archiver backend (e.g., a mounted tape drive) |
|
archiver.sql-root-folder |
${root-dir}/sql/multi-dataset-archive |
|
archiver.staging-destination |
Path to the mounted storage volume to be used for writing the container file (tar) initially, before moving it to the final destination |
|
archiver.timeout |
10800 |
Timeout in seconds after which the archiver fails to write data to the final destination |
archiver.temp-destination |
Path to the mounted storage volume to be used for storing temporary data during sanity checks |
|
archiver.unarchiving-max-waiting-time |
5 d |
Maximum time to wait in between the scheduling of an unarchiving request and the unarchiving request being finished |
archiver.unarchiving-polling-time |
1 h |
Time used to polling (querying) whether a file on the final destination is flagged as being ready to be unarchived (only used if archiver.unarchiving-wait-for-t-flag is set) |
archiver.unarchiving-prepare-command-template |
Script to run each archiver.unarchiving-polling-time days/hours/minutes/seconds to trigger the copying of the file from the tape archive to the mounted landing zone that is accessible from the openBIS node |
|
archiver.unarchiving-wait-for-t-flag |
true |
Wait for the container file (.tar) in the final destination to be have the “t” flag removed (used for tape backends that set this flag to indicate that the file has been copied from the actual tape to the mounted landing zone that is accessible from the openBIS node) |
archiver.unique-experiment-name-property-code |
${experiment-name-property-code} |
|
archiver.unique-sample-name-property-code |
${sample-name-property-code} |
|
archiver.wait-for-sanity-check-initial-waiting-time |
30 min |
Initial time to wait beofre attempting to run the sanity check on the final destination for the first time |
archiver.wait-for-sanity-check-max-waiting-time |
24 h |
Maximum time to wait for the sanity check to either return with SUCCESS or ERROR |
archiver.wait-for-sanity-check |
true |
Wait for the sanity check to return with SUCCESS (true) or not (false) |
archiver.waiting-for-free-space-polling-time |
10 min |
Time used to polling (querying) whether sufficient disk space got available on the final destination for storing the container file (.tar) |
archiver.with-sharding |
false |
Use directory sharding for the data stored on the archiving destination |
Archiving By Request Configuration (Optional)
Key |
Example Value |
Short Explanation |
|---|---|---|
multi-dataset-archiver-archiving-by-request.class |
ch.systemsx.cisd.openbis.generic.server.task.ArchivingByRequestTask |
Archiving By Request class specification |
multi-dataset-archiver-archiving-by-request.configuration-file-path |
${user-management-config-file-path} |
|
multi-dataset-archiver-archiving-by-request.interval |
10 min |
Time interval at which the Archiver attempts to archive all data sets marked as ‘archiving requested’ through invoking the ‘Request or disallow archiving’ button in the ELN |
multi-dataset-archiver-archiving-by-request.keep-in-store |
false |
Keep datasets in the openBIS store after being successfully archived (true) or delete them (false) |
multi-dataset-archiver-archiving-by-request.maximum-container-size-in-bytes |
1500000000000 |
Should match the value assigned to archiver.maximum-container-size-in-bytes |
multi-dataset-archiver-archiving-by-request.minimum-container-size-in-bytes |
10000000000 |
Should match the value assigned to archiver.minimum-container-size-in-bytes |
Miscellaneous Configuration (Optional)
Key |
Example Value |
Short Explanation |
|---|---|---|
data-set-file-name-entity-separator |
. |
|
failure-interval |
||
file-name-property-code |
file_name |
|
max-retries |
||
maintenance-tasks |
Comma-separated list of maintenance tasks to be configured for the DSS |
Screening Configuration (Optional)
Key |
Example Value |
Short Explanation |
|---|---|---|
data-source-provider |
dss-based-data-source-provider |
|
dss-based-data-source-provider.data-store-servers |
dss-screening |
|
dss-based-data-source-provider.dss-screening.database-driver |
org.postgresql.Driver |
|
dss-based-data-source-provider.dss-screening.database-url |
jdbc:postgresql://{{ openbis_local_hostname }}/imaging_productive |
AFS Modules
service.properties (Mandatory)
The service.properties contains around two dozen properties that SHOULD NOT be modified on standard production environments.
Here are ONLY discussed the ones that SHOULD BE manually configured.
Property |
Description |
|---|---|
|
Defaults to |
|
Same used by the DSS. Defaults to |
|
Same used by the DSS. |
|
Defaults to 50, a good number is: Concurrent Uploads/Downloads Web UI + 4 * Concurrent Uploads/Downloads openBIS Drive |
|
Secret password, to be shared only to those allowed to call BEGIN and PREPARE and COMMIT manually. Used for 2 Phase Transactions |
|
Secret password, to be shared only with the transaction manager to run recovery workflows. |
|
Ideally points directly to the AS in localhost http://localhost:8080 |
|
Defaults to 30000 millis, 30 sec |
|
Used by the integration plugin, should be an INSTANCE_ADMIN |
|
Password for the openBIS user |
|
Defaults to ./last-seen-deletion |
|
Defaults to 1000 |
|
Defaults to 900 seconds, 15 minutes |
service.properties (Optional)
Additionally, these are MANDATORY for Archiving but RECOMMENDED for EVERYONE, provides a cache for the immutable dataset metadata.
Values are already filled in the template, just uncomment them.
Property |
Description |
|---|---|
|
Value to be used: pathInfoFeedingTask |
|
Value to be used: ch.systemsx.cisd.etlserver.path.PathInfoDatabaseFeedingTask |
|
Value to be used: 3600 |
|
Value to be used: pathinfo |
|
Value to be used: prod |
|
Value to be used: postgresql |
|
Value to be used: ch.systemsx.cisd.openbis.dss.generic.shared.PathInfoDatabaseVersionHolder |
|
Value to be used: afs-server/sql/pathinfo |
Additionally, these are MANDATORY for setups with multiple share ids, this is for backwards compatibility with the way DSS shuffles data.
Property |
Description |
|---|---|
|
Value to be used: pathInfoFeedingTask, shufflingTask |
|
Value to be used: ch.systemsx.cisd.etlserver.plugins.SegmentedStoreShufflingTask |
|
Value to be used: 3600 |
|
Value to be used: ch.systemsx.cisd.etlserver.plugins.SimpleShuffling |
|
Value to be used: ch.systemsx.cisd.openbis.dss.generic.shared.SimpleShareFinder |
|
Value to be used: true |
Core Plugins Modules
Core Plugins modules, with few exceptions, follow the naming schema in lower-case characters:
<core-plugin>.<server-type>.<plugin-type>.<plugin-name>.<plugin-property-name>
e.g
eln-lims.as.miscellaneous.file-service.file-server.repository-path
Core Plugin |
Server Type |
Plugin Type |
Plugin Name |
Plugin Property Name |
|---|---|---|---|---|
eln-lims |
as |
miscellaneous |
file-service |
file-server.repository-path |
ELN
AS PROPERTIES
Key |
Example Value |
Short Explanation |
|---|---|---|
eln-lims.as.miscellaneous.file-service.file-server.maximum-file-size-in-MB |
50 |
|
eln-lims.as.miscellaneous.file-service.file-server.repository-path |
/data/openbis/raw-store |
Directory to be used for storing media objects such as images embedded within rich text fields in the ELN |
eln-lims.as.services.as-eln-lims-api.script-path |
||
eln-lims.as.services.freeze-api.script-path |
||
eln-lims.as.services.publication-api.script-path |
||
eln-lims.as.webapps.eln-lims.webapp-folder |
||
file-server.section_eln-lims.download-url-template |
||
file-server.section_eln-lims.error-message-template |
||
zenodo-exports-api-limit-data-size-megabytes |
4000 |
|
zenodo-exports-api-zenodoUrl |
||
zenodo-exports-api-http-proxy-url |
||
zenodo-exports-api-http-proxy-port |
||
zenodo-exports-api-accessToken |
||
eln-lims.as.services.exports-api.share-id |
||
eln-lims.as.services.exports-api.limit-data-size-megabytes |
10000 |
|
eln-lims.as.services.exports-api.research_collection.enabled |
true |
Flag for enabling ResearchCollection export form |
eln-lims.as.services.exports-api.research_collection.realm |
SWORD2 |
|
rc-exports-api-limit-data-size-megabytes |
||
rc-exports-api-service-document-url |
||
rc-exports-api-user |
||
rc-exports-api-password |
||
rc-exports-api-http-proxy-url |
||
rc-exports-api-http-proxy-port |
||
eln-lims.as.services.exports-api.sci-cat.enabled |
true |
Flag for enabling SciCat export form |
eln-lims.as.services.exports-api.sci-cat.export.url |
||
eln-lims.as.services.exports-api.sci-cat.detail.url |
||
eln-lims.as.services.exports-api.sci-cat.http.proxy.url |
||
eln-lims.as.services.exports-api.sci-cat.http.proxy.port |
||
eln-lims.as.services.exports-api.sci-cat.timeout.count |
||
eln-lims.as.services.exports-api.sci-cat.timeout.sleep |
||
eln-lims.as.services.exports-api.ro-crate.url |
||
eln-lims.as.services.search-store.script-path |
DSS PROPERTIES
Key |
Example Value |
Short Explanation |
|---|---|---|
eln-lims.dss.drop-boxes.eln-lims-dropbox.incoming-data-completeness-condition |
||
eln-lims.dss.drop-boxes.eln-lims-dropbox.top-level-data-set-handler |
||
eln-lims.dss.drop-boxes.eln-lims-dropbox.script-path |
||
eln-lims.dss.drop-boxes.eln-lims-dropbox.storage-processor |
||
eln-lims.dss.drop-boxes.eln-lims-dropbox.discard-files-patterns |
||
eln-lims.dss.drop-boxes.eln-lims-dropbox.illegal-files-patterns |
||
eln-lims.dss.drop-boxes.eln-lims-dropbox-marker.incoming-data-completeness-condition |
||
eln-lims.dss.drop-boxes.eln-lims-dropbox-marker.top-level-data-set-handler |
||
eln-lims.dss.drop-boxes.eln-lims-dropbox-marker.script-path |
||
eln-lims.dss.drop-boxes.eln-lims-dropbox-marker.storage-processor |
||
eln-lims.dss.drop-boxes.eln-lims-dropbox-marker.discard-files-patterns |
||
eln-lims.dss.drop-boxes.eln-lims-dropbox-marker.illegal-files-patterns |
||
eln-lims.dss.file-system.plugins.eln-tree.resolver-plugins.resolver-class |
||
eln-lims.dss.file-system.plugins.eln-tree.resolver-plugins.code |
||
eln-lims.dss.file-system.plugins.eln-tree.resolver-plugins.script-file |
||
eln-lims.dss.file-system.plugins.eln-tree.resolver-plugins.ftp.resolver-dev-mode |
||
eln-lims.dss.maintenance-tasks.blastdb.interval |
||
eln-lims.dss.maintenance-tasks.blastdb.dataset-types |
||
eln-lims.dss.maintenance-tasks.blastdb.entity-sequence-properties |
||
eln-lims.dss.maintenance-tasks.blastdb.file-types |
||
eln-lims.dss.maintenance-tasks.blastdb.last-seen-data-set-file |
||
eln-lims.dss.maintenance-tasks.blastdb.blast-databases-folder |
||
eln-lims.dss.maintenance-tasks.blastdb.blast-temp-folder |
||
eln-lims.dss.maintenance-tasks.blastdb.blast-tools-directory |
||
eln-lims.dss.reporting-plugins.archiving-api.sub-directory-name |
||
eln-lims.dss.reporting-plugins.archiving-api.label |
||
eln-lims.dss.reporting-plugins.dropbox-monitor-api.label |
||
eln-lims.dss.reporting-plugins.dropbox-monitor-api.script-path |
||
eln-lims.dss.reporting-plugins.dropbox-monitor-api.share-id |
||
eln-lims.dss.reporting-plugins.eln-lims-api.label |
||
eln-lims.dss.reporting-plugins.eln-lims-api.script-path |
||
eln-lims.dss.reporting-plugins.eln-lims-api.share-id |
||
eln-lims.dss.reporting-plugins.exports-api.label |
||
eln-lims.dss.reporting-plugins.exports-api.script-path |
||
eln-lims.dss.reporting-plugins.exports-api.limit-data-size-megabytes |
||
eln-lims.dss.reporting-plugins.exports-api.share-id |
||
eln-lims.dss.reporting-plugins.password-reset-api.label |
||
eln-lims.dss.reporting-plugins.password-reset-api.script-path |
||
eln-lims.dss.reporting-plugins.password-reset-api.max-delay-in-minutes |
||
eln-lims.dss.reporting-plugins.password-reset-api.password-reset-request-subject |
||
eln-lims.dss.reporting-plugins.password-reset-api.password-reset-request-body |
||
eln-lims.dss.reporting-plugins.password-reset-api.new-password-subject |
||
eln-lims.dss.reporting-plugins.password-reset-api.new-password-body |
||
eln-lims.dss.reporting-plugins.password-reset-api.share-id |
||
eln-lims.dss.reporting-plugins.rc-exports-api.label |
||
eln-lims.dss.reporting-plugins.rc-exports-api.script-path |
||
eln-lims.dss.reporting-plugins.rc-exports-api.realm |
||
eln-lims.dss.reporting-plugins.rc-exports-api.share-id |
||
eln-lims.dss.reporting-plugins.zenodo-exports-api.label |
||
eln-lims.dss.reporting-plugins.zenodo-exports-api.script-path |
||
eln-lims.dss.reporting-plugins.zenodo-exports-api.share-id |
||
eln-lims.dss.search-domain-services.blastsearch.blast-tools-directory |
||
eln-lims.dss.search-domain-services.blastsearch.blast-databases-folder |
||
dataset-uploader.h5-folders |
||
dataset-uploader.h5ar-folders |
||
default-incoming-share-id |
1 |
|
default-incoming-share-minimum-free-space-in-gb |
||
download-url |
ADMIN
AS PROPERTIES
Key |
Example Value |
Short Explanation |
More |
|---|---|---|---|
admin.as.admin-service.class |
|||
admin.as.admin-service.script-path |
|||
admin.as.webapps.webapp-folder |
DSS PROPERTIES
None.
IMAGING
AS PROPERTIES
Key |
Example Value |
Short Explanation |
|---|---|---|
eln-lims-imaging-core.as.services.imaging.python3-path |
Path to python installation (if python-based adapters are used) |
|
eln-lims-imaging-core.as.services.imaging.storageRoot.dss |
Path to dss storage root |
|
eln-lims-imaging-core.as.services.imaging.storageRoot.afs |
Path to afs storage root |
|
eln-lims-imaging-core.as.services.imaging.python-adapter.script-path |
Path to python script to be used by build-in python adapter |
|
eln-lims-imaging-core.as.services.imaging.python-adapter.python3-path |
Path to python installation to be used for build-in python adapter |
DSS PROPERTIES
None.
MONITORING-SUPPORT
AS PROPERTIES
None.
DSS PROPERTIES
Key |
Example Value |
Short Explanation |
|---|---|---|
monitoring-support.dss.reporting-plugins.dss-monitoring-initialization.label |
||
monitoring-support.dss.reporting-plugins.dss-monitoring-initialization.script-path |
||
monitoring-support.dss.reporting-plugins.dss-monitoring-initialization.share-id |
OPENBIS-SYNC
AS PROPERTIES
None.
DSS PROPERTIES
Key |
Example Value |
Short Explanation |
|---|---|---|
openbis-sync.dss.data-sources.openbis-db.databaseEngineCode |
||
openbis-sync.dss.data-sources.openbis-db.basicDatabaseName |
||
openbis-sync.dss.servlet-services.resource-sync.path |
||
openbis-sync.dss.servlet-services.resource-sync.request-handler |
||
openbis-sync.dss.servlet-services.resource-sync.request-handler.file-service-repository-path |
||
openbis-sync.dss.servlet-services.resource-sync.authentication-handler |
||
database.kind |
||
server-url |
||
download-url |
SEARCH-STORE
search-store plugin has been merged into ELN