# Unique code of this Data Store Server. Not more than 40 characters.
data-store-server-code = my-dss

# The root directory of the data store
storeroot-dir = targets/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 = 30

# Path to the keystore
keystore.path = dist/etc/openBIS.keystore

use-ssl = false

# 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.
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 = 1000

# 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 = doesnotmatter

# The base URL for Web client access.
download-url = http://localhost:8889

# SMTP properties (must start with 'mail' to be considered).
mail.smtp.host = file://targets
# mail.from = datastore_server@localhost
# mail.smtp.user = 
# mail.smtp.password = 

# Maximum number of retries if renaming failed.
# renaming.failure.max-retries = 12

# The number of milliseconds to wait before retrying to execute the renaming process.
# renaming.failure.millis-to-sleep = 5000

# 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 = 3

# ---------------------------------------------------------------------------
# reporting and processing plugins configuration
# ---------------------------------------------------------------------------

# Comma separated names of reporting plugins. Each plugin should have configuration properties prefixed with its name.
reporting-plugins = plate-image-reporter, plate-image-params-reporter, plate-image-analysis-merger, demo-reporter

# Label of the plugin which will be shown for the users.
demo-reporter.label = Show Dataset Size
# Comma separated list of dataset type codes which can be handled by this plugin.
demo-reporter.dataset-types = UNKNOWN
# Plugin class specification (together with the list of packages this class belongs to).
demo-reporter.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.demo.DemoReportingPlugin
# The property file. Its content will be passed as a parameter to the plugin.
demo-reporter.properties-file = 

# Label of the plugin which will be shown for the users.
plate-image-reporter.label = Show Plate Images
# Comma separated list of dataset type codes which can be handled by this plugin.
plate-image-reporter.dataset-types = HCS_IMAGE
# Plugin class specification (together with the list of packages this class belongs to).
plate-image-reporter.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.ScreeningImageReportingPlugin
# The property file. Its content will be passed as a parameter to the plugin.
plate-image-reporter.properties-file = 

# Label of the plugin which will be shown for the users.
plate-image-params-reporter.label = Show Plate Image Parameters
# Comma separated list of dataset type codes which can be handled by this plugin.
plate-image-params-reporter.dataset-types = HCS_IMAGE
# Plugin class specification (together with the list of packages this class belongs to).
plate-image-params-reporter.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.ScreeningPlateImageParamsReportingPlugin
# The property file. Its content will be passed as a parameter to the plugin.
plate-image-params-reporter.properties-file = 

plate-image-analysis-merger.label = Show Image Analysis Results
plate-image-analysis-merger.dataset-types = HCS_IMAGE_ANALYSIS_DATA
plate-image-analysis-merger.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.ImageAnalysisMergedRowsReportingPlugin
plate-image-analysis-merger.properties-file =

# ---------------------------------------------------------------------------

# Comma separated names of processing plugins. Each plugin should have configuration properties prefixed with its name.
processing-plugins = demo-processor

# The configuration of the processing plugin is the same as the reporting plugins configuration. 
demo-processor.label = Demo Processing
demo-processor.dataset-types = UNKNOWN
demo-processor.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.demo.DemoProcessingPlugin
demo-processor.properties-file = 

# ---------------------------------------------------------------------------

maintenance-plugins=hierarchical-storage-updater
hierarchical-storage-updater.class = ch.systemsx.cisd.etlserver.plugins.HierarchicalStorageUpdater
hierarchical-storage-updater.interval = 300
hierarchical-storage-updater.hierarchy-root-dir = targets/hierarchical-store

# ---------------------------------------------------------------------------

# list of additional web servlets which will be exposed
plugin-services = screening-image-download-servlet
# class of the web servlet
#screening-image-download-servlet.class = ch.systemsx.cisd.openbis.dss.generic.server.MergingImagesDownloadServlet
screening-image-download-servlet.class = ch.systemsx.cisd.openbis.dss.generic.server.SplittingImagesDownloadServlet
# URL which will be mapped to this servlet
screening-image-download-servlet.path = /datastore_server_screening/*

# ---------------------------------------------------------------------------

# 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=raw-data, plate-analysis-data, lmc-raw-data, lmc-jpg-data, lmc-segmented-jpg-data

# ---------------------------------------------------------------------------
# 'raw-data' thread configuration
# ---------------------------------------------------------------------------

# The directory to watch for incoming data.
raw-data.incoming-dir = targets/incoming-screening-raw
raw-data.incoming-data-completeness-condition = auto-detection

# The extractor class to use for code extraction
raw-data.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor
# Separator used to extract the barcode in the data set file name
raw-data.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator}
raw-data.data-set-info-extractor.index-of-sample-code = -1
raw-data.data-set-info-extractor.index-of-data-producer-code = 1
raw-data.data-set-info-extractor.index-of-data-production-date = 0
raw-data.data-set-info-extractor.group-code = HCS-LAB-STOCKLI

# The extractor class to use for type extraction
raw-data.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
raw-data.type-extractor.file-format-type = PNG
raw-data.type-extractor.locator-type = RELATIVE_LOCATION
raw-data.type-extractor.data-set-type = HCS_IMAGE

# The storage processor (IStorageProcessor implementation)
# raw-data.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
raw-data.storage-processor = ch.systemsx.cisd.etlserver.BDSStorageProcessor
raw-data.storage-processor.version = 1.1
raw-data.storage-processor.sampleTypeCode = PLATE
raw-data.storage-processor.sampleTypeDescription = Screening Plate
raw-data.storage-processor.format = HCS_IMAGE V1.0
raw-data.storage-processor.number_of_channels = 2
raw-data.storage-processor.contains_original_data = true
raw-data.storage-processor.well_geometry = 3x3
raw-data.storage-processor.plate_geometry = 16x24
raw-data.storage-processor.file-extractor = ch.systemsx.cisd.etlserver.imsb.HCSImageFileExtractor


# ---------------------------------------------------------------------------
# 'plate-analysis-data' thread configuration
# ---------------------------------------------------------------------------

# The directory to watch for incoming data.
plate-analysis-data.incoming-dir = targets/incoming-screening-image-analysis
plate-analysis-data.incoming-data-completeness-condition = auto-detection

# The extractor class to use for code extraction
plate-analysis-data.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor
# Separator used to extract the barcode in the data set file name
plate-analysis-data.data-set-info-extractor.entity-separator = .
plate-analysis-data.data-set-info-extractor.index-of-sample-code = 0
plate-analysis-data.data-set-info-extractor.group-code = HCS-LAB-STOCKLI

# The extractor class to use for type extraction
plate-analysis-data.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
plate-analysis-data.type-extractor.file-format-type = TSV
plate-analysis-data.type-extractor.locator-type = RELATIVE_LOCATION
plate-analysis-data.type-extractor.data-set-type = HCS_IMAGE_ANALYSIS_DATA
plate-analysis-data.type-extractor.is-measured = false

# The storage processor (IStorageProcessor implementation)
plate-analysis-data.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor


# ---------------------------------------------------------------------------
# 'LMC RAW data' thread configuration
# ---------------------------------------------------------------------------

# The directory to watch for incoming data.
lmc-raw-data.incoming-dir = targets/incoming-lmc-raw
lmc-raw-data.incoming-data-completeness-condition = auto-detection

# The extractor class to use for code extraction
lmc-raw-data.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor
# Separator used to extract the barcode in the data set file name
lmc-raw-data.data-set-info-extractor.entity-separator = .
lmc-raw-data.data-set-info-extractor.index-of-sample-code = 0
lmc-raw-data.data-set-info-extractor.index-of-data-producer-code = 
lmc-raw-data.data-set-info-extractor.group-code = LMC

# The extractor class to use for type extraction
lmc-raw-data.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
lmc-raw-data.type-extractor.file-format-type = TIFF
lmc-raw-data.type-extractor.locator-type = RELATIVE_LOCATION
lmc-raw-data.type-extractor.data-set-type = HCS_RAW_IMAGE
lmc-raw-data.type-extractor.is-measured = true

# The storage processor (IStorageProcessor implementation)
lmc-raw-data.storage-processor = ch.systemsx.cisd.etlserver.BDSStorageProcessor
lmc-raw-data.storage-processor.version = 1.1
lmc-raw-data.storage-processor.sampleTypeCode = PLATE
lmc-raw-data.storage-processor.sampleTypeDescription = Screening Plate
lmc-raw-data.storage-processor.format = HCS_IMAGE V1.0
lmc-raw-data.storage-processor.number_of_channels = 2
lmc-raw-data.storage-processor.contains_original_data = TRUE
lmc-raw-data.storage-processor.well_geometry = 3x3
lmc-raw-data.storage-processor.file-extractor = ch.systemsx.cisd.openbis.dss.lmc.HCSImageFileExtractor
lmc-raw-data.storage-processor.incoming_items_are_symbolic_link = true
lmc-raw-data.storage-processor.file_extension = tif

# ---------------------------------------------------------------------------
# 'LMC JPG data' thread configuration
# ---------------------------------------------------------------------------

# The directory to watch for incoming data.
lmc-jpg-data.incoming-dir = targets/incoming-lmc-jpg
lmc-jpg-data.incoming-data-completeness-condition = auto-detection

# The extractor class to use for code extraction
lmc-jpg-data.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor
# Separator used to extract the barcode in the data set file name
lmc-jpg-data.data-set-info-extractor.entity-separator = .
lmc-jpg-data.data-set-info-extractor.index-of-sample-code = 0
lmc-jpg-data.data-set-info-extractor.index-of-data-producer-code = 
lmc-jpg-data.data-set-info-extractor.group-code = LMC

# The extractor class to use for type extraction
lmc-jpg-data.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
lmc-jpg-data.type-extractor.file-format-type = JPG
lmc-jpg-data.type-extractor.locator-type = RELATIVE_LOCATION
#lmc-jpg-data.type-extractor.data-set-type = HCS_JPG_IMAGE
lmc-jpg-data.type-extractor.data-set-type = HCS_IMAGE
lmc-jpg-data.type-extractor.is-measured = false

# The storage processor (IStorageProcessor implementation)
lmc-jpg-data.storage-processor = ch.systemsx.cisd.etlserver.BDSStorageProcessor
lmc-jpg-data.storage-processor.version = 1.1
lmc-jpg-data.storage-processor.sampleTypeCode = PLATE
lmc-jpg-data.storage-processor.sampleTypeDescription = Screening Plate
lmc-jpg-data.storage-processor.format = HCS_IMAGE V1.0
# There is only 1 file for all channels having 2 channels merged into one image.
# We have to ignore the warning about missing channels during the upload.
lmc-jpg-data.storage-processor.number_of_channels = 2
lmc-jpg-data.storage-processor.contains_original_data = TRUE
lmc-jpg-data.storage-processor.well_geometry = 3x3
lmc-jpg-data.storage-processor.file-extractor = ch.systemsx.cisd.openbis.dss.lmc.HCSImageFileExtractor
lmc-jpg-data.storage-processor.incoming_items_are_symbolic_link = true
lmc-jpg-data.storage-processor.file_extension = jpg

# ---------------------------------------------------------------------------
# 'LMC segmented JPG data' thread configuration
# ---------------------------------------------------------------------------

# The directory to watch for incoming data.
lmc-segmented-jpg-data.incoming-dir = targets/incoming-lmc-segmented-jpg
lmc-segmented-jpg-data.incoming-data-completeness-condition = auto-detection

# The extractor class to use for code extraction
lmc-segmented-jpg-data.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor
# Separator used to extract the barcode in the data set file name
lmc-segmented-jpg-data.data-set-info-extractor.entity-separator = .
lmc-segmented-jpg-data.data-set-info-extractor.index-of-sample-code = 0
lmc-segmented-jpg-data.data-set-info-extractor.index-of-data-producer-code = 
lmc-segmented-jpg-data.data-set-info-extractor.group-code = LMC

# The extractor class to use for type extraction
lmc-segmented-jpg-data.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
lmc-segmented-jpg-data.type-extractor.file-format-type = JPG
lmc-segmented-jpg-data.type-extractor.locator-type = RELATIVE_LOCATION
#lmc-segmented-jpg-data.type-extractor.data-set-type = HCS_SEGMENTED_JPG_IMAGE
lmc-segmented-jpg-data.type-extractor.data-set-type = HCS_IMAGE
lmc-segmented-jpg-data.type-extractor.is-measured = false

# The storage processor (IStorageProcessor implementation)
lmc-segmented-jpg-data.storage-processor = ch.systemsx.cisd.etlserver.BDSStorageProcessor
lmc-segmented-jpg-data.storage-processor.version = 1.1
lmc-segmented-jpg-data.storage-processor.sampleTypeCode = PLATE
lmc-segmented-jpg-data.storage-processor.sampleTypeDescription = Screening Plate
lmc-segmented-jpg-data.storage-processor.format = HCS_IMAGE V1.0
# There is only 1 file for all channels having 2 channels merged into one image.
# We have to ignore the warning about missing channels during the upload.
lmc-segmented-jpg-data.storage-processor.number_of_channels = 2
lmc-segmented-jpg-data.storage-processor.contains_original_data = TRUE
lmc-segmented-jpg-data.storage-processor.well_geometry = 3x3
lmc-segmented-jpg-data.storage-processor.file-extractor = ch.systemsx.cisd.openbis.dss.lmc.HCSImageFileExtractor
lmc-segmented-jpg-data.storage-processor.incoming_items_are_symbolic_link = true
lmc-segmented-jpg-data.storage-processor.file_extension = jpg