added a template service.properties for screening DSS

SVN: 21219

integration-tests/templates/datastore_server_screening/etc/service.properties

+# 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 = data
+
+# 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 =
+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 =
+
+# ---------------------------------------------------------------------------
+# 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
+# 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=merged-channels-images, split-channels-images, image-analysis-results
+
+# ---------------------------------------------------------------------------
+
+# The directory to watch for incoming data.
+merged-channels-images.incoming-dir = ${incoming-root-dir}/incoming-images-merged-channels
+merged-channels-images.incoming-data-completeness-condition = auto-detection
+
+# The extractor class to use for code extraction
+merged-channels-images.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor
+merged-channels-images.data-set-info-extractor.entity-separator = .
+merged-channels-images.data-set-info-extractor.index-of-sample-code = 0
+merged-channels-images.data-set-info-extractor.index-of-data-producer-code = 
+merged-channels-images.data-set-info-extractor.space-code = ${import-space-code}
+
+# The extractor class to use for type extraction
+merged-channels-images.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
+merged-channels-images.type-extractor.file-format-type = JPG
+merged-channels-images.type-extractor.locator-type = RELATIVE_LOCATION
+merged-channels-images.type-extractor.data-set-type = HCS_IMAGE_OVERVIEW
+merged-channels-images.type-extractor.is-measured = true
+
+# Note: this storage processor is able to process folders compressed with zip as well
+merged-channels-images.storage-processor = ch.systemsx.cisd.openbis.dss.etl.PlateStorageProcessor
+# How should the original data be stored? Possible values:
+#   unchanged       - nothing is changed, the default
+#   hdf5            - all the data will be packaged into one hdf5 file
+#   hdf5_compressed - like hdf5, but each file is stored in a compressed form
+merged-channels-images.storage-processor.original-data-storage-format = unchanged
+# 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
+merged-channels-images.storage-processor.generate-thumbnails = false
+# Thumbnails size in pixels
+# merged-channels-images.storage-processor.thumbnail-max-width = 300
+# merged-channels-images.storage-processor.thumbnail-max-height = 200
+# Codes of the channels in which images have been acquired. Allowed characters: [A-Z0-9_-]. 
+# Number and order of entries must be consistent with 'channel-labels'.
+merged-channels-images.storage-processor.channel-codes = GFP, DAPI
+# Labels of the channels in which images have been acquired. 
+# Number and order of entries must be consistent with 'channel-codes'.
+merged-channels-images.storage-processor.channel-labels = Gfp, Dapi
+
+# Optional boolean property, true by default. 
+# Set to false to allow datasets in one experiment to use different channels.
+# In this case 'channel-codes' and 'channel-labels' become optional and are used only to determine the label for each channel code.
+# It should be set to 'false' for overlay image datasets. 
+#merged-channels-images.storage-processor.define-channels-per-experiment = false
+
+# Optional boolean property, true by default. 
+# If true an email is sent if some images for the uploaded plate are missing. 
+#merged-channels-images.storage-processor.notify-if-incomplete = false
+
+# Optional boolean property, true by default. 
+# If set to false then the dataset whcih cannot be registered will be left in the incoming folder 
+# and will be mentioned in the .faulty_paths file
+#merged-channels-images.storage-processor.move-unregistered-datasets-to-error-dir = false
+    
+# This is an optional boolean property which defines if all image datasets in one experiment have the same
+# channels or if each imported dataset can have different channels. By default true if not specified.
+#merged-channels-images.storage-processor.define-channels-per-experiment = false
+# Format: [width]>x[height], e.g. 3x4. Specifies the grid into which a microscope divided the well to acquire images.
+merged-channels-images.storage-processor.well_geometry = 3x3
+# implementation of the IHCSImageFileExtractor interface which maps images to the location on the plate and particular channel
+# Here: the extractor requireds that each image name should adhere to the schema:
+#     <any-text>_<plate-code>_<well-code>_<tile-code>_<channel-name>.<allowed-image-extension>
+merged-channels-images.storage-processor.file-extractor = ch.systemsx.cisd.openbis.dss.etl.HCSImageFileExtractor
+# specification of the imaging db
+merged-channels-images.storage-processor.data-source = imaging-db
+# Optional comma separated list of color components. 
+# Available values: RED, GREEN or BLUE. 
+# If specified then the channels are extracted from the color components and override 'file-extractor' results.
+merged-channels-images.storage-processor.extract-single-image-channels = GREEN, BLUE
+
+# ---------------------------------------------------------------------------
+
+# The directory to watch for incoming data.
+split-channels-images.incoming-dir = ${incoming-root-dir}/incoming-images-split-channels
+split-channels-images.incoming-data-completeness-condition = auto-detection
+
+# The extractor class to use for code extraction
+split-channels-images.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor
+split-channels-images.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator}
+split-channels-images.data-set-info-extractor.index-of-sample-code = -1
+split-channels-images.data-set-info-extractor.index-of-data-producer-code = 1
+split-channels-images.data-set-info-extractor.index-of-data-production-date = 0
+split-channels-images.data-set-info-extractor.space-code = ${import-space-code}
+
+# The extractor class to use for type extraction
+split-channels-images.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
+split-channels-images.type-extractor.file-format-type = JPG
+split-channels-images.type-extractor.locator-type = RELATIVE_LOCATION
+split-channels-images.type-extractor.data-set-type = HCS_IMAGE_OVERVIEW
+split-channels-images.type-extractor.is-measured = true
+
+split-channels-images.storage-processor = ch.systemsx.cisd.openbis.dss.etl.PlateStorageProcessor
+split-channels-images.storage-processor.generate-thumbnails = false
+# The first specified channel will be blue, the second will be green and the third will be red.
+# If there are more channels, combinations of colors will be used.
+split-channels-images.storage-processor.channel-codes = GFP, DAPI
+split-channels-images.storage-processor.channel-labels = Gfp, Dapi
+split-channels-images.storage-processor.well_geometry = 3x3
+split-channels-images.storage-processor.file-extractor = ch.systemsx.cisd.openbis.dss.etl.HCSImageFileExtractor
+split-channels-images.storage-processor.data-source = imaging-db
+
+# ---------------------------------------------------------------------------
+
+# The directory to watch for incoming data.
+image-analysis-results.incoming-dir = ${incoming-root-dir}/incoming-analysis
+image-analysis-results.incoming-data-completeness-condition = auto-detection
+
+# The extractor class to use for code extraction
+image-analysis-results.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor
+# Separator used to extract the barcode in the data set file name
+image-analysis-results.data-set-info-extractor.entity-separator = .
+image-analysis-results.data-set-info-extractor.index-of-sample-code = 0
+image-analysis-results.data-set-info-extractor.space-code = ${import-space-code}
+
+# The extractor class to use for type extraction
+image-analysis-results.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
+image-analysis-results.type-extractor.file-format-type = CSV
+image-analysis-results.type-extractor.locator-type = RELATIVE_LOCATION
+image-analysis-results.type-extractor.data-set-type = HCS_ANALYSIS_WELL_FEATURES
+image-analysis-results.type-extractor.is-measured = false
+
+# The storage processor (IStorageProcessor implementation)
+image-analysis-results.storage-processor = ch.systemsx.cisd.openbis.dss.etl.featurevector.FeatureVectorStorageProcessor
+image-analysis-results.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
+image-analysis-results.storage-processor.data-source = imaging-db
+# semi-colon (;) by default 
+image-analysis-results.storage-processor.separator = ,
+image-analysis-results.storage-processor.ignore-comments = true
+image-analysis-results.storage-processor.well-name-row = row
+image-analysis-results.storage-processor.well-name-col = col
+image-analysis-results.storage-processor.well-name-col-is-alphanum = true
+
+# --- Example configuration of a dropbox for images which are not connected to wells on the plate
+
+# The directory to watch for incoming data.
+#microscopy-dropbox.incoming-dir = ${incoming-root-dir}/incoming-microscopy
+#microscopy-dropbox.incoming-data-completeness-condition = auto-detection
+
+# The extractor class to use for code extraction
+#microscopy-dropbox.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor
+#microscopy-dropbox.data-set-info-extractor.entity-separator = .
+#microscopy-dropbox.data-set-info-extractor.index-of-sample-code = 0
+#microscopy-dropbox.data-set-info-extractor.space-code = ${import-space-code}
+
+# The extractor class to use for type extraction
+#microscopy-dropbox.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
+#microscopy-dropbox.type-extractor.file-format-type = TIFF
+#microscopy-dropbox.type-extractor.locator-type = RELATIVE_LOCATION
+#microscopy-dropbox.type-extractor.data-set-type = MICROSCOPY_IMAGE
+#microscopy-dropbox.type-extractor.is-measured = true
+
+#microscopy-dropbox.storage-processor = ch.systemsx.cisd.openbis.dss.etl.MicroscopyStorageProcessor
+#microscopy-dropbox.storage-processor.file-extractor = ch.systemsx.cisd.openbis.dss.etl.MicroscopyImageFileExtractor
+#microscopy-dropbox.storage-processor.data-source = imaging-db
+#microscopy-dropbox.storage-processor.channel-names = BLUE, GREEN, RED
+#microscopy-dropbox.storage-processor.well_geometry = 2x3
+#microscopy-dropbox.storage-processor.tile_mapping = 1,2,3;4,5,6
+
+# --- Microscopy dropbox with a series of images with any names ---------------------------
+
+# The directory to watch for incoming data.
+#microscopy-series-dropbox.incoming-dir = ${incoming-root-dir}/incoming-microscopy-series
+#microscopy-series-dropbox.incoming-data-completeness-condition = auto-detection
+
+# The extractor class to use for code extraction
+#microscopy-series-dropbox.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor
+#microscopy-series-dropbox.data-set-info-extractor.entity-separator = .
+#microscopy-series-dropbox.data-set-info-extractor.index-of-sample-code = 0
+#microscopy-series-dropbox.data-set-info-extractor.space-code = ${import-space-code}
+
+# The extractor class to use for type extraction
+#microscopy-series-dropbox.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
+#microscopy-series-dropbox.type-extractor.file-format-type = TIFF
+#microscopy-series-dropbox.type-extractor.locator-type = RELATIVE_LOCATION
+#microscopy-series-dropbox.type-extractor.data-set-type = MICROSCOPY_IMAGE
+#microscopy-series-dropbox.type-extractor.is-measured = true
+
+#microscopy-series-dropbox.storage-processor = ch.systemsx.cisd.openbis.dss.etl.MicroscopyBlackboxSeriesStorageProcessor
+#microscopy-series-dropbox.storage-processor.data-source = imaging-db