# 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 = targets/playground/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 # 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/openbis # The username to use when contacting the openBIS server username = etlserver # The password to use when contacting the openBIS server password = etlserver # The base URL for Web client access. download-url = https://localhost:${port} # 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 = 10 # Globally used separator character which separates entities in a data set file name data-set-file-name-entity-separator = : # 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. # reprocess-faulty-datasets = false # --------------------------------------------------------------------------- # 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 = illumina-summary # Label of the plugin which will be shown for the users. illumina-summary.label = Illumina Summary # Comma separated list of dataset type codes which can be handled by this plugin. illumina-summary.dataset-types = SHORT_READS_SEQUENCING, ILLUMINA_GA_OUTPUT # Plugin class specification (together with the list of packages this class belongs to). illumina-summary.class = ch.ethz.bsse.cisd.dsu.dss.plugins.IlluminaSummaryReportingPlugin # The property file. Its content will be passed as a parameter to the plugin. illumina-summary.properties-file = # 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 = flow-cell, fl1, fl2, fl3, fl4, fl5, fl6, fl7, fl8, default default.incoming-dir = targets/playground/default_upload default.incoming-data-completeness-condition = auto-detection default.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor default.data-set-info-extractor.strip-file-extension = true default.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator} default.data-set-info-extractor.space-code = BSSE_FLOWCELLS default.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor default.type-extractor.file-format-type = PROPRIETARY default.type-extractor.locator-type = RELATIVE_LOCATION default.type-extractor.data-set-type = ILLUMINA_GA_OUTPUT default.type-extractor.is-measured = true default.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor default.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor # --------------------------------------------------------------------------- # 'flow-cell' thread configuration # --------------------------------------------------------------------------- # The directory to watch for incoming data. flow-cell.incoming-dir = targets/playground/incoming-flow-cell # 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'. flow-cell.incoming-data-completeness-condition = auto-detection # 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). # flow-cell.space-code = # ---------------- Plugin properties # The extractor class to use for code extraction flow-cell.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor flow-cell.data-set-info-extractor.strip-file-extension = true flow-cell.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator} flow-cell.data-set-info-extractor.space-code = BSSE # Location of file containing data set properties #flow-cell.data-set-info-extractor.data-set-properties-file-name = data-set.properties # The extractor class to use for type extraction flow-cell.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor flow-cell.type-extractor.file-format-type = PROPRIETARY flow-cell.type-extractor.locator-type = RELATIVE_LOCATION flow-cell.type-extractor.data-set-type = ILLUMINA_GA_OUTPUT flow-cell.type-extractor.is-measured = true # The storage processor (IStorageProcessor implementation) flow-cell.storage-processor = ch.ethz.bsse.cisd.dsu.dss.StorageProcessor flow-cell.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor flow-cell.storage-processor.flow-lane-drop-box-template = targets/playground/drop-box-{0} flow-cell.storage-processor.entity-separator = ${data-set-file-name-entity-separator} flow-cell.storage-processor.transfer.FMI = targets/playground/drop-box-fmi flow-cell.storage-processor.meta-data-file-prefix = PREFIX_FOR_TSV # -------- Flow Lane 1 -------------------------------------- fl1.incoming-dir = targets/playground/drop-box-1 fl1.data-set-info-extractor = ch.ethz.bsse.cisd.dsu.dss.FlowLaneDataSetInfoExtractor fl1.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator} fl1.data-set-info-extractor.index-of-space-code = 0 fl1.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor fl1.type-extractor.file-format-type = SRF fl1.type-extractor.data-set-type = SRF_PER_LANE fl1.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor # -------- Flow Lane 2 -------------------------------------- fl2.incoming-dir = targets/playground/drop-box-2 fl2.data-set-info-extractor = ch.ethz.bsse.cisd.dsu.dss.FlowLaneDataSetInfoExtractor fl2.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator} fl2.data-set-info-extractor.index-of-space-code = 0 fl2.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor fl2.type-extractor.file-format-type = SRF fl2.type-extractor.data-set-type = SRF_PER_LANE fl2.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor # -------- Flow Lane 3 -------------------------------------- fl3.incoming-dir = targets/playground/drop-box-3 fl3.data-set-info-extractor = ch.ethz.bsse.cisd.dsu.dss.FlowLaneDataSetInfoExtractor fl3.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator} fl3.data-set-info-extractor.index-of-space-code = 0 fl3.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor fl3.type-extractor.file-format-type = SRF fl3.type-extractor.data-set-type = SRF_PER_LANE fl3.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor # -------- Flow Lane 4 -------------------------------------- fl4.incoming-dir = targets/playground/drop-box-4 fl4.data-set-info-extractor = ch.ethz.bsse.cisd.dsu.dss.FlowLaneDataSetInfoExtractor fl4.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator} fl4.data-set-info-extractor.index-of-space-code = 0 fl4.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor fl4.type-extractor.file-format-type = SRF fl4.type-extractor.data-set-type = SRF_PER_LANE fl4.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor # -------- Flow Lane 5 -------------------------------------- fl5.incoming-dir = targets/playground/drop-box-5 fl5.data-set-info-extractor = ch.ethz.bsse.cisd.dsu.dss.FlowLaneDataSetInfoExtractor fl5.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator} fl5.data-set-info-extractor.index-of-space-code = 0 fl5.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor fl5.type-extractor.file-format-type = SRF fl5.type-extractor.data-set-type = SRF_PER_LANE fl5.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor # -------- Flow Lane 6 -------------------------------------- fl6.incoming-dir = targets/playground/drop-box-6 fl6.data-set-info-extractor = ch.ethz.bsse.cisd.dsu.dss.FlowLaneDataSetInfoExtractor fl6.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator} fl6.data-set-info-extractor.index-of-space-code = 0 fl6.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor fl6.type-extractor.file-format-type = SRF fl6.type-extractor.data-set-type = SRF_PER_LANE fl6.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor # -------- Flow Lane 7 -------------------------------------- fl7.incoming-dir = targets/playground/drop-box-7 fl7.data-set-info-extractor = ch.ethz.bsse.cisd.dsu.dss.FlowLaneDataSetInfoExtractor fl7.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator} fl7.data-set-info-extractor.index-of-space-code = 0 fl7.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor fl7.type-extractor.file-format-type = SRF fl7.type-extractor.data-set-type = SRF_PER_LANE fl7.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor # -------- Flow Lane 8 -------------------------------------- fl8.incoming-dir = targets/playground/drop-box-8 fl8.data-set-info-extractor = ch.ethz.bsse.cisd.dsu.dss.FlowLaneDataSetInfoExtractor fl8.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator} fl8.data-set-info-extractor.index-of-space-code = 0 fl8.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor fl8.type-extractor.file-format-type = SRF fl8.type-extractor.data-set-type = SRF_PER_LANE fl8.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor