# Unique code of this Data Store Server. Not more than 40 characters. data-store-server-code = dss-screening # host name of the machine on which the datastore server is running host-address = https://localhost # parent directory of the store directory and all the dropboxes root-dir = $DSS.ROOT-DIR # The root directory of the data store storeroot-dir = ${root-dir}/store # The directory where the command queue file is located; defaults to storeroot-dir commandqueue-dir = # Port port = 8444 use-ssl = true # 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 = ${host-address}:8443 # The username to use when contacting the openBIS server username = etlserver # The password for the etlserver user who contacts the openBIS server password = etlserver_password # The base URL for Web client access to the data store server. download-url = ${host-address}:${port} # SMTP properties (must start with 'mail' to be considered). # The current configuration saves the emails in the file system in the root directory mail.smtp.host = file://${root-dir} # mail.smtp.host = localhost # mail.from = datastore_server@ethz.ch # mail.smtp.user = # mail.smtp.password = # --------------------------------------------------------------------------- # (optional) archiver configuration # --------------------------------------------------------------------------- # Configuration of an archiver task. All properties are prefixed with 'archiver.'. # Archiver class specification (together with the list of packages this class belongs to). #archiver.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.demo.DemoArchiver # --------------------------------------------------------------------------- # INTERNAL CONFIGURATION, # Do not change this part unless you are developing openBIS extensions. # --------------------------------------------------------------------------- # --------------------------------------------------------------------------- # screening database specification # --------------------------------------------------------------------------- data-sources = imaging-db imaging-db.version-holder-class = ch.systemsx.cisd.openbis.dss.etl.ImagingDatabaseVersionHolder imaging-db.databaseEngineCode = postgresql imaging-db.basicDatabaseName = imaging imaging-db.databaseKind = productive imaging-db.scriptFolder = sql imaging-db.owner =${DB.USERNAME} imaging-db.password = ${DB.PASSWORD} # Credentials of a database user which is able to create a new database or roles in it. # Leave empty to use the db engines defaults. # Used only during the first start of the server or when server is upgraded to a new version. imaging-db.adminUser = ${DB.ADMIN.USERNAME} imaging-db.adminPassword = ${DB.ADMIN.PASSWORD} # --------------------------------------------------------------------------- # reporting and processing plugins configuration # --------------------------------------------------------------------------- # Comma separated names of reporting plugins. Each plugin should have configuration properties prefixed with its name. reporting-plugins = default-plate-image-analysis, plate-image-analysis-graph default-plate-image-analysis.label = Image Analysis Results default-plate-image-analysis.dataset-types = HCS_ANALYSIS_WELL_FEATURES default-plate-image-analysis.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.ImageAnalysisMergedRowsReportingPlugin default-plate-image-analysis.properties-file = plate-image-analysis-graph.label = Image Analysis Graphs plate-image-analysis-graph.dataset-types = HCS_ANALYSIS_WELL_FEATURES plate-image-analysis-graph.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.ImageAnalysisGraphReportingPlugin plate-image-analysis-graph.servlet-path = datastore_server_graph/ plate-image-analysis-graph.properties-file = etc/tabular-data-graph.properties # --------------------------------------------------------------------------- # screening specific extension servlets # --------------------------------------------------------------------------- # list of additional web servlets which will be exposed plugin-services = screening-image-download-servlet, tabular-data-graph-servlet, screening-dss-api-exporter-servlet # class of the web servlet screening-image-download-servlet.class = ch.systemsx.cisd.openbis.dss.generic.server.MergingImagesDownloadServlet # URL which will be mapped to this servlet screening-image-download-servlet.path = /datastore_server_screening/* tabular-data-graph-servlet.class = ch.systemsx.cisd.openbis.dss.generic.server.TabularDataGraphServlet tabular-data-graph-servlet.path = /datastore_server_graph/* tabular-data-graph-servlet.properties-file = etc/tabular-data-graph.properties # expose an DSS API interface with RPC screening-dss-api-exporter-servlet.class = ch.systemsx.cisd.openbis.dss.generic.server.DssScreeningApiServlet screening-dss-api-exporter-servlet.path = /rmi-datastore-server-screening-api-v1/* # --------------------------------------------------------------------------- # 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 = microscopy-image-overview microscopy-image-overview.class = ch.systemsx.cisd.openbis.dss.generic.server.MergingImagesDownloadServlet microscopy-image-overview.dataset-types = MICROSCOPY_IMAGE # --------------------------------------------------------------------------- maintenance-plugins=data-set-clean-up # hierarchical-storage-updater # the plugin which is run periodically to create a mirror structure of the store with the same files # but with user-readable structure of directories hierarchical-storage-updater.class = ch.systemsx.cisd.etlserver.plugins.HierarchicalStorageUpdater # specified in seconds. Here : every day hierarchical-storage-updater.interval = 86400 hierarchical-storage-updater.hierarchy-root-dir = ${root-dir}/hierarchical-store # Removes data sets deleted from openBIS also from imaging database data-set-clean-up.class = ch.systemsx.cisd.etlserver.plugins.DeleteFromExternalDBMaintenanceTask # specified in seconds. Here : every day data-set-clean-up.interval = 86400 data-set-clean-up.data-source = imaging-db # --------------------------------------------------------------------------- # DROPBOXES CONFIGURATION # --------------------------------------------------------------------------- incoming-root-dir = ${root-dir} # 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 = 300 # code of the default space in openBIS to which the data will be imported import-space-code = DEMO # 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=simple-dropbox # --------------------------------------------------------------------------- # --------------------------------------------------------------------------- # --- Jython dropbox for HCS images ----------------------------------------------- # --------------------------------------------------------------------------- # The directory to watch for incoming data. simple-dropbox.incoming-dir = ${incoming-root-dir}/incoming-simple simple-dropbox.incoming-data-completeness-condition = auto-detection # The extractor class to use for code extraction simple-dropbox.top-level-data-set-handler = ch.systemsx.cisd.openbis.dss.etl.jython.JythonPlateDataSetHandler simple-dropbox.script-path = ${incoming-root-dir}/dropboxes/simple-dropbox.py simple-dropbox.storage-processor = ch.systemsx.cisd.openbis.dss.etl.PlateStorageProcessor simple-dropbox.storage-processor.data-source = imaging-db #images-hcs-jython-dropbox.storage-processor.file-extractor = ch.systemsx.cisd.openbis.dss.etl.jython.JythonImageFileExtractor simple-dropbox.storage-processor.define-channels-per-experiment = false # -- Should the thumbnails be generated? # It slows down the dataset registration, but increases the performance when the user wants to see the image. # Can be 'true' or 'false', 'false' is the default value # mimages-hcs-jython-dropbox.storage-processor.generate-thumbnails = false # images-hcs-jython-dropbox.storage-processor.compress-thumbnails = true