# Unique code of this Data Store Server. Not more than 40 characters. data-store-server-code = standard root-dir = targets # The root directory of the data store storeroot-dir = ${root-dir}/store # The directory for incoming files over rpc rpc-incoming-dir = ${root-dir}/incoming-rpc core-plugins-folder = source/core-plugins # 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 # The minimum time (in seconds) of availability of the data stream since the time when user requested # for the data stream url. If not specified default value (20 seconds) will be used. # data-stream-timeout = 20 # 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 # Time out for accessing openBIS server. Default value is 5 minutes. server-timeout-in-minutes = 10 # The location of the jars accessable to web start clients webstart-jar-path = targets/dist/datastore_server/lib # 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://${root-dir}/email mail.from = datastore_server@localhost mail.smtp.user = mail.smtp.password = # If this property is set a test e-mail will be sent to the specified address after DSS successfully started-up. mail.test.address = test@localhost # --------------------------------------------------------------------------- # Data sources data-sources = path-info-db # Data source for pathinfo database 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.databaseKind = dev path-info-db.scriptFolder = ../datastore_server/source/sql # --------------------------------------------------------------------------- # 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, hcs-viewer, hcs-viewer-tiff, default-hcs-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. # Wildcards are allowed, but the DSS server may need to be restarted if a new data set type is added to openBIS demo-reporter.dataset-types = .* # 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 = # Optional properties: # - separator of values in the file, significant for TSV and CSV files; default: tab #tsv-viewer.separator = ; # - whether lines beginning with '#' should be ignored by the plugin; default: true #tsv-viewer.ignore-comments = false # - excel sheet name or index (0 based) used for the excel file (.xsl or .xslx); default: 0 (first sheet) #tsv-viewer.excel-sheet = example_sheet_name 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 = , hcs-viewer.label = HCS PNG hcs-viewer.dataset-types = HCS_IMAGE hcs-viewer.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.GenericDssLinkReportingPlugin hcs-viewer.download-url = ${download-url} hcs-viewer.data-set-regex = .*/PNG/.*\.jpg hcs-viewer.data-set-path = original hcs-viewer-tiff.label = HCS TIFF hcs-viewer-tiff.dataset-types = HCS_IMAGE hcs-viewer-tiff.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.GenericDssLinkReportingPlugin hcs-viewer-tiff.download-url = ${download-url} hcs-viewer-tiff.data-set-regex = .*/TIFF/.*\.jpg hcs-viewer-tiff.data-set-path = original default-hcs-viewer.label = Default HCS View default-hcs-viewer.dataset-types = HCS_IMAGE default-hcs-viewer.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.GenericDssLinkReportingPlugin default-hcs-viewer.download-url = ${download-url} default-hcs-viewer.data-set-regex = .*\.jpg # 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 # Wildcards are allowed, but the DSS server may need to be restarted if a new data set type is added to openBIS demo-processor.dataset-types = HCS_.*, CONTAINER_.* 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, simple-thread, hdf5-thread, dss-system-test-thread # True if incoming directories should be created on server startup if they don't exist. # Default - false (server will fail at startup if one of incoming directories doesn't exist). incoming-dir-create = true # --------------------------------------------------------------------------- # Dataset uploader 'main-thread' configuration # --------------------------------------------------------------------------- # The directory to watch for incoming data. main-thread.incoming-dir = ${root-dir}/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 = auto-detection # 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.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 # Path to the script that will be executed after successful data set registration. # The script will be called with two parameters: and (in the data store). # main-thread.post-registration-script = /example/scripts/my-script.sh # The directory to watch for incoming data. tsv-thread.incoming-dir = ${root-dir}/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 = ${root-dir}/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 # The directory to watch for incoming data. simple-thread.incoming-dir = ${root-dir}/incoming-simple simple-thread.incoming-data-completeness-condition = auto-detection simple-thread.strip-file-extension = true simple-thread.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor # The extractor plugin class to use for code extraction simple-thread.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor # Separator used to extract the barcode in the data set file name simple-thread.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator} simple-thread.data-set-info-extractor.strip-file-extension = true simple-thread.data-set-info-extractor.space-code = CISD simple-thread.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor simple-thread.type-extractor.file-format-type = TIFF simple-thread.type-extractor.locator-type = RELATIVE_LOCATION simple-thread.type-extractor.data-set-type = HCS_IMAGE # The directory to watch for incoming data. hdf5-thread.incoming-dir = ${root-dir}/incoming-hdf5 hdf5-thread.incoming-data-completeness-condition = auto-detection hdf5-thread.strip-file-extension = true hdf5-thread.storage-processor = ch.systemsx.cisd.etlserver.hdf5.HDF5StorageProcessor # The extractor plugin class to use for code extraction hdf5-thread.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor # Separator used to extract the barcode in the data set file name hdf5-thread.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator} hdf5-thread.data-set-info-extractor.strip-file-extension = true hdf5-thread.data-set-info-extractor.space-code = SPACE hdf5-thread.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor hdf5-thread.type-extractor.file-format-type = HDF5 hdf5-thread.type-extractor.locator-type = RELATIVE_LOCATION hdf5-thread.type-extractor.data-set-type = HCS_IMAGE dss-system-test-thread.incoming-dir = ${root-dir}/incoming-simple dss-system-test-thread.incoming-data-completeness-condition = auto-detection dss-system-test-thread.strip-file-extension = true dss-system-test-thread.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor # The extractor plugin class to use for code extraction dss-system-test-thread.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor # Separator used to extract the barcode in the data set file name dss-system-test-thread.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator} dss-system-test-thread.data-set-info-extractor.strip-file-extension = true dss-system-test-thread.data-set-info-extractor.space-code = CISD dss-system-test-thread.data-set-info-extractor.data-set-properties-file-name = data-set.properties dss-system-test-thread.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor dss-system-test-thread.type-extractor.file-format-type = TIFF dss-system-test-thread.type-extractor.locator-type = RELATIVE_LOCATION dss-system-test-thread.type-extractor.data-set-type = HCS_IMAGE # --------------------------------------------------------------------------- # (optional) image overview plugins configuration # --------------------------------------------------------------------------- # Comma separated names of image overview plugins. # Each plugin should have configuration properties prefixed with its name. # Generic properties for each include: # .class - Fully qualified plugin class name (mandatory). # .default - If true all data set types not handled by other plugins should be handled # by the plugin (default = false). # .dataset-types - Comma separated list of data set types handled by the plugin # (optional and ignored if default is true, otherwise mandatory). overview-plugins = default-overview, hcs-image-overview default-overview.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.demo.DemoOverviewPlugin default-overview.default = true # Optional property specific to the plugin default-overview.label = default plugin hcs-image-overview.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.demo.DemoOverviewPlugin hcs-image-overview.dataset-types = HCS_IMAGE hcs-image-overview.label = plugin for HCS_IMAGE # --------------------------------------------------------------------------- # (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 archiver.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.RsyncArchiver # dectination of the archive (can be local or remote) # local: #archiver.destination = openbis:tmp/dest # remote: archiver.destination = /Users/openbis/dest # indicates if data should be synchronized when local copy differs from one in archive (default: true) archiver.synchronize-archive = true archiver.batch-size-in-bytes = 20000000 # --------------------------------------------------------------------------- # 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) # .execute-only-once - If true the task will be executed exactly once, # interval will be ignored. By default set to false. maintenance-plugins = auto-archiver, path-info-deletion, post-registration #maintenance-plugins = auto-archiver, path-info-feeding # 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 # use this policy to archive datasets in batches grouped by experiment # auto-archiver.policy.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.archiver.ByExpermientPolicy # the min-size in bytes, default is 0 #auto-archiver.policy.minimal-archive-size = # the max-size in bytes, default is 2^63-1. #auto-archiver.policy.maximal-archive-size = # Maintenance task (performed only once) to create paths of existing data sets in pathinfo database path-info-feeding.class = ch.systemsx.cisd.etlserver.path.PathInfoDatabaseFeedingTask path-info-feeding.execute-only-once = true # Maintenance task for deleting entries in pathinfo database after deletion of data sets path-info-deletion.class = ch.systemsx.cisd.etlserver.plugins.DeleteFromExternalDBMaintenanceTask path-info-deletion.interval = 120 path-info-deletion.data-source = path-info-db path-info-deletion.data-set-perm-id = CODE # Maintenance task for post registration of all paths of a freshly registered data set to be fed into pathinfo database post-registration.class = ch.systemsx.cisd.etlserver.postregistration.PostRegistrationMaintenanceTask post-registration.interval = 30 post-registration.cleanup-tasks-folder = targets/cleanup-tasks # The following date should the day when the DDS is started up the first time with PathInfoDatabaseFeedingTask. # After PathInfoDatabaseFeedingTask has been performed it can be removed and the following line can be deleted. #post-registration.ignore-data-sets-before-date = 2011-04-18 post-registration.last-seen-data-set-file = targets/last-seen-data-set 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 jython-version=2.7 # Typical options to disable coping general, owner and group permissions # rsync-options = --no-p --no-o --no-g