# Unique code of this Data Store Server. Not more than 40 characters. data-store-server-code = DSS1 # The root directory of the data store storeroot-dir = data/store # The directory where the command queue file is located; defaults to storeroot-dir commandqueue-dir = # Port port = 8444 # Session timeout in minutes session-timeout = 720 # Path to the keystore keystore.path = etc/openBIS.keystore # Password of the keystore keystore.password = changeit # Key password of the keystore keystore.key-password = changeit # The check interval (in seconds) check-interval = 60 # The time-out for clean up work in the shutdown sequence (in seconds). # Note that that the maximal time for the shutdown sequence to complete can be as large # as twice this time. # Remark: On a network file system, it is not recommended to turn this value to something # lower than 180. shutdown-timeout = 180 # If free disk space goes below value defined here, a notification email will be sent. # Value must be specified in kilobytes (1048576 = 1024 * 1024 = 1GB). If no high water mark is # specified or if value is negative, the system will not be watching. highwater-mark = -1 # If a data set is successfully registered it sends out an email to the registrator. # If this property is not specified, no email is sent to the registrator. This property # does not affect the mails which are sent, when the data set could not be registered. notify-successful-registration = false # The URL of the openBIS server server-url = http://localhost:8888/openbis # The username to use when contacting the openBIS server username = etlserver # The password to use when contacting the openBIS server password = etlserver # # CIFEX configuration: Only needed if data export should work without the user having to type in # his password. Note that in in order for this to work the CIFEX server needs to be configured to # allow calling setSessionUser() from the IP address of this data store server, see configuration # option allowed-ips-for-set-session-user in CIFEX's service.properties # # The admin username to use when contacting the CIFEX server cifex-admin-username = # The admin password to use when contacting the CIFEX server cifex-admin-password = # The base URL for Web client access. download-url = https://localhost:8444 # SMTP properties (must start with 'mail' to be considered). # mail.smtp.host = localhost # mail.from = datastore_server@localhost # ---------------- Timing parameters for file system operations on remote shares. # Time (in seconds) to wait for any file system operation to finish. Operations exceeding this # timeout will be terminated. timeout = 60 # Number of times that a timed out operation will be tried again (0 means: every file system # operation will only ever be performed once). max-retries = 11 # Time (in seconds) to wait after an operation has been timed out before re-trying. failure-interval = 10 # The period of no write access that needs to pass before an incoming data item is considered # complete and ready to be processed (in seconds) [default: 300]. # Valid only when auto-detection method is used to determine if an incoming data are ready to be processed. # quiet-period = # Globally used separator character which separates entities in a data set file name data-set-file-name-entity-separator = _ # --------------------------------------------------------------------------- # reporting and processing plugins configuration # --------------------------------------------------------------------------- # Comma separated names of reporting plugins. Each plugin should have configuration properties prefixed with its name. # If name has 'default-' prefix it will be used by default in data set Data View. reporting-plugins = demo-reporter # Label of the plugin which will be shown for the users. demo-reporter.label = Show Dataset Size # Comma separated list of dataset type codes which can be handled by this plugin. demo-reporter.dataset-types = UNKNOWN # Plugin class specification (together with the list of packages this class belongs to). demo-reporter.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.demo.DemoReportingPlugin # The property file. Its content will be passed as a parameter to the plugin. demo-reporter.properties-file = # Comma separated names of processing plugins. Each plugin should have configuration properties prefixed with its name. processing-plugins = demo-processor # The configuration of the processing plugin is the same as the reporting plugins configuration. demo-processor.label = Demo Processing demo-processor.dataset-types = UNKNOWN demo-processor.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.demo.DemoProcessingPlugin demo-processor.properties-file = # Data set validators used to accept or reject data sets to be registered. # Comma separated list of validator definitions. data-set-validators = validator # Definition of data set validator 'validator' validator.data-set-type = HCS_IMAGE validator.path-patterns = **/*.txt validator.columns = id, description, size validator.id.header-pattern = ID validator.id.mandatory = true validator.id.order = 1 validator.id.value-type = unique validator.description.header-pattern = Description validator.description.value-type = string validator.description.value-pattern = .{0,100} validator.size.header-pattern = A[0-9]+ validator.size.can-define-multiple-columns = true validator.size.allow-empty-values = true validator.size.value-type = numeric validator.site.value-range = [0,Infinity) # Comma separated names of processing threads. Each thread should have configuration properties prefixed with its name. # E.g. 'code-extractor' property for the thread 'my-etl' should be specified as 'my-etl.code-extractor' inputs=main-thread # --------------------------------------------------------------------------- # 'main-thread' thread configuration # --------------------------------------------------------------------------- # The directory to watch for incoming data. main-thread.incoming-dir = data/incoming # If 'true' then unidentified and invalid data sets will be deleted instead of being moved to 'unidentified' folder # Allowed values: # - false - (default) move unidentified or invalid data sets to 'unidentified' folder # - true - delete unidentified or invalid data sets # delete-unidentified = true # Determines when the incoming data should be considered complete and ready to be processed. # Allowed values: # - auto-detection - when no write access will be detected for a specified 'quite-period' # - marker-file - when an appropriate marker file for the data exists. # The default value is 'marker-file'. main-thread.incoming-data-completeness-condition = marker-file # The space the samples extracted by this thread belong to. If commented out or empty, then samples # are considered associated to a database instance (not space private). # main-thread.space-code = # --------------------------------------------------------------------------- # maintenance plugins configuration # --------------------------------------------------------------------------- # Comma separated names of maintenance plugins. # Each plugin should have configuration properties prefixed with its name. # Mandatory properties for each include: # .class - Fully qualified plugin class name # .interval - The time between plugin executions (in seconds) # Optional properties for each include: # .start - Time of the first execution (HH:mm) #maintenance-plugins = # Creates hierarchical version of the data store, based on the content of the database #hierarchy-builder.class = ch.systemsx.cisd.etlserver.plugins.HierarchicalStorageUpdater # The time between rebuilding the hierarchical store structure (in seconds) #hierarchy-builder.interval = 86400 # The root directory of the hierarchical data store #hierarchy-builder.hierarchy-root-dir = data/hierarchical-store # ---------------- Plugin properties # The extractor class to use for code extraction main-thread.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor # Separator used to extract the barcode in the data set file name main-thread.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator} # The index of the sample code in the name when splitted by the entity-separator #main-thread.index-of-sample-code = -1 # The index of the codes of parent data sets (leave that commented out to _not_ have a data set parent) #index-of-parent-data-set-codes = -2 # The space main-thread.data-set-info-extractor.space-code = TEST # Location of file containing data set properties #main-thread.data-set-info-extractor.data-set-properties-file-name = data-set.properties # IDataSetInfoExtractor working with CIFEX DataStoreTrigger # main-thread.data-set-info-extractor = ch.systemsx.cisd.etlserver.cifex.CifexDataSetInfoExtractor # The extractor class to use for type extraction main-thread.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor main-thread.type-extractor.file-format-type = TIFF main-thread.type-extractor.locator-type = RELATIVE_LOCATION main-thread.type-extractor.data-set-type = HCS_IMAGE main-thread.type-extractor.is-measured = true # ITypeExtractor working with CIFEX DataStoreTrigger # main-thread.type-extractor = ch.systemsx.cisd.etlserver.cifex.CifexTypeExtractor # main-thread.type-extractor.locator-type = RELATIVE_LOCATION # main-thread.type-extractor.is-measured = true # The storage processor (IStorageProcessor implementation) main-thread.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor # main-thread.storage-processor = ch.systemsx.cisd.etlserver.BDSStorageProcessor # main-thread.storage-processor.version = 1.1 # main-thread.storage-processor.sampleTypeCode = CELL_PLATE # main-thread.storage-processor.sampleTypeDescription = Screening Plate # main-thread.storage-processor.format = UNKNOWN V1.0 # IStorageProcessor deleting files not matching specified regular expression # main-thread.storage-processor = ch.systemsx.cisd.etlserver.CifexStorageProcessor # main-thread.storage-processor.keep-file-regex = .*(?