Skip to content
Snippets Groups Projects
Commit 7b519616 authored by tpylak's avatar tpylak
Browse files

LMS-1546 screening: clear and organize configuration 

SVN: 16646
parent 012eb8cb
No related branches found
No related tags found
No related merge requests found
Expand all Hide whitespace changes
Inline Side-by-side
screening/dist/etc/service.properties
+ 173
− 89
View file @ 7b519616
# Unique code of this Data Store Server. Not more than 40 characters.
data-store-server-code = my-dss
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 = targets/store
storeroot-dir = ${root-dir}/store
# The directory where the command queue file is located; defaults to storeroot-dir
commandqueue-dir =
# Port
port = 8889
use-ssl = true
# Session timeout in minutes
session-timeout = 30
session-timeout = 720
# Path to the keystore
keystore.path = dist/etc/openBIS.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 = 5
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.
shutdown-timeout = 2
# 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 = 1048576
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
......@@ -41,37 +48,41 @@ highwater-mark = 1048576
notify-successful-registration = false
# The URL of the openBIS server
server-url = http://localhost:8888/openbis
server-url = ${host-address}:8443
# The username to use when contacting the openBIS server
username = etlserver_imsb
username = etlserver
# The password to use when contacting the openBIS server
password = doesnotmatter
# The password for the etlserver user who contacts the openBIS server
password = etlserver_password
# The base URL for Web client access.
download-url = http://localhost:8889
# The base URL for Web client access to the data store server.
download-url = ${host-address}:8444
# SMTP properties (must start with 'mail' to be considered).
mail.smtp.host = file://targets
# mail.from = datastore_server@localhost
# The current configuration saves the emails in the file system in the root directory
mail.smtp.host = file://${root-dir}
# mail.smtp.host = localhost
# mail.from = datastore_server@ethz.ch
# mail.smtp.user =
# mail.smtp.password =
# Maximum number of retries if renaming failed.
# renaming.failure.max-retries = 12
# ---------------------------------------------------------------------------
# (optional) archiver configuration
# ---------------------------------------------------------------------------
# The number of milliseconds to wait before retrying to execute the renaming process.
# renaming.failure.millis-to-sleep = 5000
# Configuration of an archiver task. All properties are prefixed with 'archiver.'.
# Globally used separator character which separates entities in a data set file name
data-set-file-name-entity-separator = _
# 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
# 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
# ---------------------------------------------------------------------------
# INTERNAL CONFIGURATION,
# Do not change this part unless you are developing openBIS extensions.
# ---------------------------------------------------------------------------
# ---------------------------------------------------------------------------
# screening database specification
# ---------------------------------------------------------------------------
data-sources = imaging-db
......@@ -86,108 +97,181 @@ imaging-db.scriptFolder = sql
# ---------------------------------------------------------------------------
# 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, demo-reporter
reporting-plugins = default-plate-image-analysis, plate-image-analysis-graph, plate-image-params-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 =
default-plate-image-analysis.label = Image Analysis Results
default-plate-image-analysis.dataset-types = HCS_IMAGE_ANALYSIS_DATA, HCS_ANALYSIS_PER_GENE
default-plate-image-analysis.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.ImageAnalysisMergedRowsReportingPlugin
default-plate-image-analysis.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.demo.ScreeningImageReportingPlugin
# The property file. Its content will be passed as a parameter to the plugin.
plate-image-reporter.properties-file =
plate-image-analysis-graph.label = Image Analysis Graphs
plate-image-analysis-graph.dataset-types = HCS_IMAGE_ANALYSIS_DATA, HCS_ANALYSIS_PER_GENE
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
# Label of the plugin which will be shown for the users.
plate-image-params-reporter.label = Show Plate Image Parameters
plate-image-params-reporter.label = 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.demo.ScreeningPlateImageParamsReportingPlugin
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 =
# ---------------------------------------------------------------------------
# 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/*
# Comma separated names of processing plugins. Each plugin should have configuration properties prefixed with its name.
processing-plugins = demo-processor
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
# 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 =
# 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/*
# ---------------------------------------------------------------------------
maintenance-plugins=hierarchical-storage-updater, data-set-clean-up
maintenance-plugins=hierarchical-storage-updater, data-set-clean-up, migrator
# 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
hierarchical-storage-updater.interval = 120
hierarchical-storage-updater.hierarchy-root-dir = targets/hierarchical-store
# 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.DataSetDeletionMaintenanceTask
data-set-clean-up.interval = 30
# specified in seconds. Here : every day
data-set-clean-up.interval = 86400
data-set-clean-up.data-source = imaging-db
migrator.class = ch.systemsx.cisd.etlserver.plugins.ChainedDataSetMigrationTask
migrator.execute-only-once = true
migrator.storeRoot = ${storeroot-dir}
migrator.migrators = bds-image-db, bds-original-relocator, bds-remover
migrator.bds-image-db.class = ch.systemsx.cisd.openbis.dss.etl.bdsmigration.BDSImagingDatabaseMigrator
migrator.bds-image-db.data-source = imaging-db
migrator.bds-image-db.channel-names = dapi, gfp
#migrator.bds-image-db.extract-single-image-channels = BLUE, GREEN
migrator.bds-original-relocator.class = ch.systemsx.cisd.openbis.dss.etl.bdsmigration.BDSOriginalDataRelocatorMigrator
migrator.bds-remover.class = ch.systemsx.cisd.openbis.dss.etl.bdsmigration.BDSDataRemoverMigrator
# ---------------------------------------------------------------------------
# DROPBOXES CONFIGURATION
# ---------------------------------------------------------------------------
# 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.ImagesDownloadServlet
# URL which will be mapped to this servlet
screening-image-download-servlet.path = /datastore_server_screening/*
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
# 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
inputs=split-channels-images, merged-channels-images, image-analysis-results, genedata-merged-channels-images, genedata-image-analysis-results
# ---------------------------------------------------------------------------
# 'raw-data' thread configuration
# 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 = DEMO
# 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
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 = true
split-channels-images.storage-processor.channel-names = blue, green
split-channels-images.storage-processor.well_geometry = 3x3
split-channels-images.storage-processor.deprecated-file-extractor = ch.systemsx.cisd.etlserver.imsb.HCSImageFileExtractor
split-channels-images.storage-processor.data-source = imaging-db
# ---------------------------------------------------------------------------
# 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 = DEMO
# 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
merged-channels-images.type-extractor.is-measured = true
merged-channels-images.storage-processor = ch.systemsx.cisd.openbis.dss.etl.PlateStorageProcessor
merged-channels-images.storage-processor.generate-thumbnails = true
#merged-channels-images.storage-processor.thumbnail-max-width = 300
#merged-channels-images.storage-processor.thumbnail-max-height = 200
merged-channels-images.storage-processor.channel-names = green, blue
merged-channels-images.storage-processor.well_geometry = 3x3
merged-channels-images.storage-processor.file-extractor = ch.systemsx.cisd.openbis.dss.etl.lmc.HCSImageFileExtractor
merged-channels-images.storage-processor.data-source = imaging-db
# Available values: RED, BLUE or GREEN
merged-channels-images.storage-processor.extract-single-image-channels = GREEN, BLUE
# ---------------------------------------------------------------------------
# The directory to watch for incoming data.
raw-data.incoming-dir = targets/incoming-screening-raw
raw-data.incoming-data-completeness-condition = auto-detection
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
raw-data.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor
image-analysis-results.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 = IMSB
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 = DEMO
# 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
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_IMAGE_ANALYSIS_DATA
image-analysis-results.type-extractor.is-measured = false
# 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
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
screening/dist/etc/tabular-data-graph.properties 0 → 100644
+ 37
− 0
View file @ 7b519616
# ------------------------------------------------------------------
# Properties File For Generating Graphs From Tabular Data
# ------------------------------------------------------------------
# The width of the full image
full-width = 800
# The height of the full image
full-height = 600
# The width of the table column
column-width = 300
# The height of the table row
column-height = 200
# The graphs shown per row
graphs = graph1, graph2, graph3
# The properties for the first scatter plot
graph1.graph-type = scatterplot
graph1.x-axis = <x axis feature name, e.g. TotalCells>
graph1.y-axis = <y axis feature name, e.g. InfectedCells>
graph1.title = <title, e.g. Total vs. Infected>
# The properties for the histogram
graph2.graph-type = histogram
graph2.column = <feature name, e.g. TotalCells>
graph2.number-of-bins = 20
graph2.title = <title, e.g. Total Cells Histogram>
# The properties for the heatmap
graph3.graph-type = heatmap
graph3.x-axis = <name of the column which contains plate row number, e.g. row or WellName>
graph3.y-axis = <name of the column which contains plate column number, e.g. col or WellName>
graph3.column = <feature name, e.g. InfectionIndex>
graph3.title = <title, e.g. Infection Index>
screening/etc/service.properties
+ 174
− 337
View file @ 7b519616
This diff is collapsed.
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment