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# Unique code of this Data Store Server. Not more than 40 characters.
data-store-server-code = BASYNTHEC
# The root directory of the data store
storeroot-dir = ${data-folder}/store
# The directory for incoming files over rpc
rpc-incoming-dir = ${data-folder}/incoming
# 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 = 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 = https://localhost:8443
# 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:8444
# 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
# ---------------------------------------------------------------------------
# INTERNAL CONFIGURATION,
# Do not change this part unless you are developing openBIS extensions.
# ---------------------------------------------------------------------------
# ---------------------------------------------------------------------------
# reporting and processing plugins configuration
# ---------------------------------------------------------------------------
# Comma separated names of reporting plugins. Each plugin should have configuration properties prefixed with its name.
reporting-plugins = tsv-viewer
tsv-viewer.label = Time Series
tsv-viewer.dataset-types = HCS_IMAGE_ANALYSIS_DATA
tsv-viewer.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.TSVViewReportingPlugin
# ---------------------------------------------------------------------------
# BEGIN DROPBOXES
# ---------------------------------------------------------------------------
# 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, metabolomics, growth-profiles, transcriptomics, proteomics
# ---------------------------------------------------------------------------
# main thread configuration
# ---------------------------------------------------------------------------
main-thread.incoming-dir = ${root}/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
main-thread.delete-unidentified = true
main-thread.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler
main-thread.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
main-thread.script-path = /local0/openbis/jython_scripts/data-set-handler.py
main-thread.validation-script-path = /local0/openbis/jython_scripts/data-set-validator.py
# ---------------------------------------------------------------------------
# metabolomics thread configuration
# ---------------------------------------------------------------------------
metabolomics.incoming-dir = ${root}/incoming-metabolomics
metabolomics.incoming-data-completeness-condition = auto-detection
metabolomics.delete-unidentified = true
metabolomics.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler
metabolomics.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
metabolomics.script-path = /local0/openbis/jython_scripts/metabolomics/data-set-handler.py
metabolomics.validation-script-path = /local0/openbis/jython_scripts/metabolomics/data-set-validator.py
# ---------------------------------------------------------------------------
# growth-profiles thread configuration
# ---------------------------------------------------------------------------
growth-profiles.incoming-dir = ${root}/incoming-od600
growth-profiles.incoming-data-completeness-condition = auto-detection
growth-profiles.delete-unidentified = true
growth-profiles.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler
growth-profiles.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
growth-profiles.script-path = /local0/openbis/jython_scripts/growth-profiles/data-set-handler.py
growth-profiles.validation-script-path = /local0/openbis/jython_scripts/growth-profiles/data-set-validator.py
# ---------------------------------------------------------------------------
# transcriptomics thread configuration
# ---------------------------------------------------------------------------
transcriptomics.incoming-dir = ${root}/incoming-transcriptomics
transcriptomics.incoming-data-completeness-condition = auto-detection
transcriptomics.delete-unidentified = true
transcriptomics.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler
transcriptomics.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
transcriptomics.script-path = /local0/openbis/jython_scripts/transcriptomics/data-set-handler.py
transcriptomics.validation-script-path = /local0/openbis/jython_scripts/transcriptomics/data-set-validator.py
# ---------------------------------------------------------------------------
# proteomics thread configuration
# ---------------------------------------------------------------------------
proteomics.incoming-dir = ${root}/incoming-proteomics
proteomics.incoming-data-completeness-condition = auto-detection
proteomics.delete-unidentified = true
proteomics.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler
proteomics.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
proteomics.script-path = /local0/openbis/jython_scripts/proteomics/data-set-handler.py
proteomics.validation-script-path = /local0/openbis/jython_scripts/proteomics/data-set-validator.py
#
# The dss-rpc section configures the RPC put functionality by providing a mapping between data
# set type and input thread parameters.
#
# The default input thread is specified by the put-default key. If not specified, the first input
# thread will be used.
#
# Mappings are specified by dss-rpc.<data-set-code> = <thread-name>
#
# If this section is empty, then the first input thread will be used.
#
dss-rpc.put-default = main-thread
dss-rpc.put.METABOLITE_INTENSITIES = metabolomics
dss-rpc.put.OD600 = growth-profiles
dss-rpc.put.TRANSCRIPTOMICS = transcriptomics
dss-rpc.put.PROTEIN_QUANTIFICATIONS = proteomics