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# Unique code of this Data Store Server. Not more than 40 characters.
data-store-server-code = DSS1
# host name of the machine on which the datastore server is running
# parent directory of the store directory and all the dropboxes
# 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)
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# 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 = openbis-dss@localhost
# 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, data-source
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
imaging-db.owner =
imaging-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 =
imaging-db.adminPassword =
data-source.databaseEngineCode = postgresql
data-source.basicDatabaseName = proteomics
data-source.databaseKind = productive
# ---------------------------------------------------------------------------
# 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 <plugin> include:
# <plugin>.class - Fully qualified plugin class name (mandatory).
# <plugin>.default - If true all data set types not handled by other plugins should be handled
# by the plugin (default = false).
# <plugin>.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,data-set-clean-up-proteomics
# 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.openbis.dss.etl.DeleteFromImagingDBMaintenanceTask
# specified in seconds. Here : every day
data-set-clean-up.interval = 86400
data-set-clean-up.data-source = imaging-db
data-set-clean-up-proteomics.class = ch.systemsx.cisd.etlserver.plugins.DeleteFromExternalDBMaintenanceTask
data-set-clean-up-proteomics.interval = 300
data-set-clean-up-proteomics.data-source = data-source
data-set-clean-up-proteomics.data-set-table-name = data_sets
# ---------------------------------------------------------------------------
# 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.
# 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, hcs-dropbox, ms-injection, ms-search
# ---------------------------------------------------------------------------
# ---------------------------------------------------------------------------
# ---------- Dropbox for unspecified data -----------------------------------
# ---------------------------------------------------------------------------
simple-dropbox.incoming-dir = ${incoming-root-dir}/incoming-simple
simple-dropbox.incoming-data-completeness-condition = auto-detection
simple-dropbox.top-level-data-set-handler = ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler
simple-dropbox.script-path = ${incoming-root-dir}/dropboxes/simple-dropbox.py
simple-dropbox.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
# ---------------------------------------------------------------------------
# ---------------------------------------------------------------------------
# ---------- Dropbox for HCS images -----------------------------------------
# ---------------------------------------------------------------------------
hcs-dropbox.incoming-dir = ${incoming-root-dir}/incoming-hcs
hcs-dropbox.incoming-data-completeness-condition = auto-detection
hcs-dropbox.top-level-data-set-handler = ch.systemsx.cisd.openbis.dss.etl.jython.JythonPlateDataSetHandler
hcs-dropbox.script-path = ${incoming-root-dir}/dropboxes/hcs-dropbox.py
hcs-dropbox.storage-processor = ch.systemsx.cisd.openbis.dss.etl.PlateStorageProcessor
hcs-dropbox.storage-processor.data-source = imaging-db
hcs-dropbox.storage-processor.define-channels-per-experiment = false
# ---------------------------------------------------------------------------
# 'ms-injection' drop box for spectra data
# ---------------------------------------------------------------------------
# The directory to watch for incoming data.
ms-injection.incoming-dir = ${incoming-root-dir}/incoming-ms-injection
# 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'.
ms-injection.incoming-data-completeness-condition = auto-detection
ms-injection.data-set-info-extractor = ch.systemsx.cisd.openbis.etlserver.proteomics.DataSetInfoExtractorForMSInjection
ms-injection.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
ms-injection.type-extractor = ch.systemsx.cisd.openbis.etlserver.proteomics.TypeExtractorForMSInjection
# ---------------------------------------------------------------------------
# 'ms-search' drop box for spectra data
# ---------------------------------------------------------------------------
# The directory to watch for incoming data.
ms-search.incoming-dir = ${incoming-root-dir}/incoming-ms-search
# 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'.
ms-search.incoming-data-completeness-condition = auto-detection
ms-search.data-set-info-extractor = ch.systemsx.cisd.openbis.etlserver.proteomics.DataSetInfoExtractorForProteinResults
ms-search.data-set-info-extractor.separator = +
ms-search.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
ms-search.type-extractor.file-format-type = XML
ms-search.type-extractor.locator-type = RELATIVE_LOCATION
ms-search.type-extractor.data-set-type = PROT_RESULT
ms-search.type-extractor.is-measured = false
ms-search.storage-processor = ch.systemsx.cisd.openbis.etlserver.proteomics.StorageProcessorWithResultDataSetUploader
ms-search.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
ms-search.storage-processor.assuming-extended-prot-xml = false
ms-search.storage-processor.database.basic-name = ${data-source.basicDatabaseName}
ms-search.storage-processor.database.kind = ${data-source.databaseKind}
ms-search.storage-processor.database.owner =
ms-search.storage-processor.database.password =