# Unique code of this Data Store Server. Not more than 40 characters. data-store-server-code = standard # The root directory of the data store storeroot-dir = targets/store # The directory where the command queue file is located; defaults to storeroot-dir commandqueue-dir = # Port port = 8889 # Session timeout in minutes session-timeout = 30 # Set to 'false' for development/testing without deployed server. In this mode datastore will not use # SSL when connecting to openbis. Otherwise all 'keystore' properties need to be set for SSL connection # (default when use-ssl property is not set so there is no need to specify it on production servers). use-ssl = false # Path, password and key password for SSL connection #keystore.path = dist/etc/openBIS.keystore #keystore.password = changeit #keystore.key-password = changeit # The check interval (in seconds) check-interval = 5 # 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. shutdown-timeout = 2 # 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 = 1048576 # 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 = doesnotmatter # # 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 = http://localhost:8889 # SMTP properties (must start with 'mail' to be considered). mail.smtp.host = file://targets/email mail.from = datastore_server@localhost mail.smtp.user = mail.smtp.password = # Maximum number of retries if renaming failed. # renaming.failure.max-retries = 12 # The number of milliseconds to wait before retrying to execute the renaming process. # renaming.failure.millis-to-sleep = 5000 # Globally used separator character which separates entities in a data set file name data-set-file-name-entity-separator = _ # 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 = 3 # --------------------------------------------------------------------------- # 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, tsv-viewer, csv-viewer # 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 = HCS_IMAGE # 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 = tsv-viewer.label = TSV View tsv-viewer.dataset-types = TSV tsv-viewer.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.TSVViewReportingPlugin tsv-viewer.properties-file = csv-viewer.label = CSV View csv-viewer.dataset-types = CSV csv-viewer.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.TSVViewReportingPlugin csv-viewer.separator = , # 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 = HCS_IMAGE 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, tsv-thread, csv-thread # --------------------------------------------------------------------------- # Dataset uploader 'main-thread' configuration # --------------------------------------------------------------------------- # The directory to watch for incoming data. main-thread.incoming-dir = targets/incoming # Specifies what should happen if an error occurs during dataset processing. # By default this flag is set to false and user has to modify the 'faulty paths file' # each time the faulty dataset should be processed again. # Set this flag to true if the processing should be repeated after some time without manual intervention. # Note that this can increase the server load. # main-thread.reprocess-faulty-datasets = false # 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 store format that should be applied in the incoming directory. main-thread.incoming-dir.format = # The extractor plugin 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} #main-thread.data-set-info-extractor.space-code = CISD # Location of file containing data set properties #main-thread.data-set-info-extractor.data-set-properties-file-name = data-set.properties 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 # 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 = HCS_IMAGE V1.0 main-thread.storage-processor.number_of_channels = 2 main-thread.storage-processor.contains_original_data = TRUE main-thread.storage-processor.well_geometry = 3x3 main-thread.storage-processor.file-extractor = ch.systemsx.cisd.etlserver.imsb.HCSImageFileExtractor # The directory to watch for incoming data. tsv-thread.incoming-dir = targets/incoming-tsv tsv-thread.incoming-data-completeness-condition = auto-detection tsv-thread.strip-file-extension = true tsv-thread.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor # The extractor plugin class to use for code extraction tsv-thread.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor # Separator used to extract the barcode in the data set file name tsv-thread.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator} tsv-thread.data-set-info-extractor.strip-file-extension = true #main-thread.data-set-info-extractor.space-code = CISD # Location of file containing data set properties #main-thread.data-set-info-extractor.data-set-properties-file-name = data-set.properties tsv-thread.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor tsv-thread.type-extractor.file-format-type = TSV tsv-thread.type-extractor.locator-type = RELATIVE_LOCATION tsv-thread.type-extractor.data-set-type = TSV csv-thread.incoming-dir = targets/incoming-csv csv-thread.incoming-data-completeness-condition = auto-detection csv-thread.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor # The extractor plugin class to use for code extraction csv-thread.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor # Separator used to extract the barcode in the data set file name csv-thread.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator} csv-thread.data-set-info-extractor.strip-file-extension = true csv-thread.data-set-info-extractor.space-code = CISD # Location of file containing data set properties #main-thread.data-set-info-extractor.data-set-properties-file-name = data-set.properties csv-thread.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor csv-thread.type-extractor.file-format-type = CSV csv-thread.type-extractor.locator-type = RELATIVE_LOCATION csv-thread.type-extractor.data-set-type = CSV # --------------------------------------------------------------------------- # (optional) archiver configuration # --------------------------------------------------------------------------- # Configuration of an archiver task. All properties are prefixed with 'archiver.'. # Archiver class specification (together with the list of packages this class belongs to). archiver.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.demo.DemoArchiver # --------------------------------------------------------------------------- # 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 = auto-archiver # Performs automatic archivization of 'ACTIVE' data sets based on their properties auto-archiver.class = ch.systemsx.cisd.etlserver.plugins.AutoArchiverTask # The time between subsequent archivizations (in seconds) auto-archiver.interval = 10 # Time of the first execution (HH:mm) auto-archiver.start = 23:00 # following properties are optional # only data sets of specified type will be archived #auto-archiver.data-set-type = UNKNOWN # only data sets that are older than specified number of days will be archived (default = 0) #auto-archiver.older-than = 90 # fully qualified class name of a policy that additionally filters data sets to be filtered #auto-archiver.policy.class = ch.systemsx.cisd.etlserver.plugins.DummyAutoArchiverPolicy