# Unique code of this Data Store Server. Not more than 40 characters. data-store-server-code = DSS1 data-folder = targets/playground/data # The root directory of the data store storeroot-dir = ${data-folder}/store # The directory where the command queue file is located; defaults to storeroot-dir commandqueue-dir = # Port port = 8889 # Session timeout in minutes session-timeout = 720 # Set to 'false' for development/testing without deployed server. In this mode datastore will not use # SSL when connecting to openbis. Otherwise all 'keystore' properties need to be set for SSL connection # (default when use-ssl property is not set so there is no need to specify it on production servers). use-ssl = false # Path to the keystore keystore.path = ../datastore_server/dist/etc/openBIS.keystore # Password of the keystore keystore.password = changeit # Key password of the keystore keystore.key-password = changeit # The check interval (in seconds) check-interval = 5 # The time-out for clean up work in the shutdown sequence (in seconds). # Note that that the maximal time for the shutdown sequence to complete can be as large # as twice this time. # Remark: On a network file system, it is not recommended to turn this value to something # lower than 180. shutdown-timeout = 2 # If free disk space goes below value defined here, a notification email will be sent. # Value must be specified in kilobytes (1048576 = 1024 * 1024 = 1GB). If no high water mark is # specified or if value is negative, the system will not be watching. highwater-mark = -1 # If a data set is successfully registered it sends out an email to the registrator. # If this property is not specified, no email is sent to the registrator. This property # does not affect the mails which are sent, when the data set could not be registered. notify-successful-registration = false # The URL of the openBIS server server-url = http://localhost:8888 # The username to use when contacting the openBIS server username = etlserver_csb # The password to use when contacting the openBIS server password = etlserver_csb # The base URL for Web client access. download-url = http://localhost:${port} # SMTP properties (must start with 'mail' to be considered). mail.smtp.host = file://targets/playground/email 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 = 10 # 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,cifex # --------------------------------------------------------------------------- # main thread configuration # --------------------------------------------------------------------------- # The directory to watch for incoming data. main-thread.incoming-dir = ${data-folder}/incoming # 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 # ---------------- Plugin properties # The extractor class to use for code extraction main-thread.data-set-info-extractor = ch.systemsx.cisd.etlserver.DataSetInfoExtractorWithFileNameProperty main-thread.data-set-info-extractor.extractor = ch.ethz.bsse.cisd.plasmid.dss.ParentDirectoryDataSetInfoExtractor main-thread.data-set-info-extractor.extractor.extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor main-thread.data-set-info-extractor.extractor.extractor.space-code = YEAST_LAB # The extractor class to use for type extraction main-thread.type-extractor = ch.ethz.bsse.cisd.plasmid.dss.PlasmidTypeExtractor main-thread.type-extractor.dataset-types = SEQ_FILE: gb fasta xdna fa, RAW_DATA: ab1 main-thread.type-extractor.file-types = GB: gb, FASTA: fasta, XDNA: xdna, FA: fa, AB1: ab1 main-thread.type-extractor.default-file-type = PROPRIETARY main-thread.type-extractor.directory-file-type = DIRECTORY # The storage processor (IStorageProcessor implementation) main-thread.storage-processor = ch.ethz.bsse.cisd.plasmid.dss.PlasmidStorageProcessor main-thread.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor # path to the root directory of the server where PlasMapper is deployed (webapps in jetty) main-thread.storage-processor.plasmapper-root-dir = /Users/buczekp/CISD/cifex/jetty/webapps # the base URL of PlasMapper web application main-thread.storage-processor.plasmapper-base-url = http://localhost:8082/PlasMapper # The dataset handler (IDataSetHandler implementation) main-thread.dataset-handler = ch.ethz.bsse.cisd.plasmid.dss.PlasmidDataSetHandler # --------------------------------------------------------------------------- # 'cifex' thread configuration # --------------------------------------------------------------------------- cifex.incoming-dir = ${data-folder}/incoming-cifex cifex.incoming-data-completeness-condition = auto-detection cifex.delete-unidentified = true cifex.data-set-info-extractor = ch.systemsx.cisd.etlserver.DataSetInfoExtractorWithFileNameProperty cifex.data-set-info-extractor.strip-extension = true cifex.data-set-info-extractor.extractor = ch.systemsx.cisd.etlserver.cifex.CifexDataSetInfoExtractor cifex.type-extractor = ch.systemsx.cisd.etlserver.cifex.CifexTypeExtractor cifex.storage-processor = ch.systemsx.cisd.etlserver.CifexStorageProcessor cifex.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor cifex.storage-processor.keep-file-regex = .*(?