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Commit 01512819 authored by felmer's avatar felmer
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LMS-2766 fixing service.propertie for DSS 

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openbis_standard_technologies/dist/core-plugins/.gitignore 0 → 100644
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openbis_standard_technologies/dist/etc/service.properties
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......@@ -2,10 +2,10 @@
data-store-server-code = DSS1
# host name of the machine on which the datastore server is running
host-address = https://localhost
host-address = https://$HOSTNAME
# parent directory of the store directory and all the dropboxes
root-dir = data
root-dir = $DSS_ROOT_DIR
# The root directory of the data store
storeroot-dir = ${root-dir}/store
......@@ -28,7 +28,7 @@ keystore.password = changeit
keystore.key-password = changeit
# The check interval (in seconds)
check-interval = 60
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
......@@ -194,196 +194,37 @@ 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
quiet-period = 10
# 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, ms-injection, ms-search
inputs=simple-dropbox, hcs-dropbox, ms-injection, ms-search
# ---------------------------------------------------------------------------
# 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
# ---------------------------------------------------------------------------
# ---------- 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
# 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
# ---------------------------------------------------------------------------
# ---------------------------------------------------------------------------
# ---------- 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
......@@ -398,12 +239,12 @@ ms-injection.incoming-dir = ${incoming-root-dir}/incoming-ms-injection
# 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.phosphonetx.DataSetInfoExtractorForMSInjection
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.phosphonetx.TypeExtractorForMSInjection
ms-injection.type-extractor = ch.systemsx.cisd.openbis.etlserver.proteomics.TypeExtractorForMSInjection
# ---------------------------------------------------------------------------
# 'ms-search' drop box for protein data
# 'ms-search' drop box for spectra data
# ---------------------------------------------------------------------------
# The directory to watch for incoming data.
ms-search.incoming-dir = ${incoming-root-dir}/incoming-ms-search
......@@ -415,7 +256,7 @@ ms-search.incoming-dir = ${incoming-root-dir}/incoming-ms-search
# 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.phosphonetx.DataSetInfoExtractorForProteinResults
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
......@@ -424,7 +265,7 @@ 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.phosphonetx.StorageProcessorWithResultDataSetUploader
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}
......@@ -432,3 +273,4 @@ ms-search.storage-processor.database.kind = ${data-source.databaseKind}
ms-search.storage-processor.database.owner =
ms-search.storage-processor.database.password =
openbis_standard_technologies/dist/tarball/installer/dss-service.properties
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# ---------------------------------------------------------------------------
# Standard technologies specific properties.
# ---------------------------------------------------------------------------
root-dir = $DSS_ROOT_DIR
storeroot-dir = $DSS_ROOT_DIR/store
host-address = https://$HOSTNAME
quiet-period = 10
check-interval = 5
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