From ec8ed5ebce4743e22769dc351ea4d5f55eb02e0e Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Fri, 25 Jun 2010 11:36:59 +0000
Subject: [PATCH] LMS-1546 unify devel and dist screening config
SVN: 16737
---
screening/etc/service.properties | 115 ++++++++++++++++++-------------
1 file changed, 66 insertions(+), 49 deletions(-)
diff --git a/screening/etc/service.properties b/screening/etc/service.properties
index 1719cd48f1d..a366eea8f75 100644
--- a/screening/etc/service.properties
+++ b/screening/etc/service.properties
@@ -139,7 +139,8 @@ screening-dss-api-exporter-servlet.path = /rmi-datastore-server-screening-api-v1
# ---------------------------------------------------------------------------
-maintenance-plugins=hierarchical-storage-updater, data-set-clean-up, migrator, feature-migrator
+maintenance-plugins=data-set-clean-up
+# hierarchical-storage-updater, feature-migrator, bds-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
@@ -154,16 +155,17 @@ data-set-clean-up.class = ch.systemsx.cisd.etlserver.plugins.DataSetDeletionMain
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
+bds-migrator.class = ch.systemsx.cisd.etlserver.plugins.ChainedDataSetMigrationTask
+bds-migrator.execute-only-once = true
+bds-migrator.storeRoot = ${storeroot-dir}
+#bds-migrator.migrators = bds-image-db, bds-original-relocator, bds-remover
+bds-migrator.migrators = bds-image-db
+bds-migrator.bds-image-db.class = ch.systemsx.cisd.openbis.dss.etl.bdsmigration.BDSImagingDatabaseMigrator
+bds-migrator.bds-image-db.data-source = imaging-db
+bds-migrator.bds-image-db.channel-names = dapi, gfp
+#bds-migrator.bds-image-db.extract-single-image-channels = BLUE, GREEN
+bds-migrator.bds-original-relocator.class = ch.systemsx.cisd.openbis.dss.etl.bdsmigration.BDSOriginalDataRelocatorMigrator
+bds-migrator.bds-remover.class = ch.systemsx.cisd.openbis.dss.etl.bdsmigration.BDSDataRemoverMigrator
feature-migrator.class = ch.systemsx.cisd.etlserver.plugins.ChainedDataSetMigrationTask
feature-migrator.execute-only-once = true
@@ -194,37 +196,12 @@ data-set-file-name-entity-separator = _
# Valid only when auto-detection method is used to determine if an incoming data are ready to be processed.
quiet-period = 3
+# 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=split-channels-images, merged-channels-images, image-analysis-results, genedata-merged-channels-images, genedata-image-analysis-results
-
-# ---------------------------------------------------------------------------
-
-# 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
+inputs=merged-channels-images, split-channels-images, image-analysis-results, genedata-merged-channels-images, genedata-image-analysis-results
# ---------------------------------------------------------------------------
@@ -237,7 +214,7 @@ merged-channels-images.data-set-info-extractor = ch.systemsx.cisd.etlserver.Defa
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 = LIBRARY_TEST
+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
@@ -247,18 +224,58 @@ 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
+# 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
+# Names of the channels in which images have been acquired.
+merged-channels-images.storage-processor.channel-names = gfp, dapi
+# 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
-# Available values: RED, BLUE or GREEN
+# 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
+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
+split-channels-images.storage-processor.channel-names = 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
@@ -268,7 +285,7 @@ image-analysis-results.data-set-info-extractor = ch.systemsx.cisd.etlserver.Defa
# 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 = DEMO
+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
@@ -302,7 +319,7 @@ genedata-merged-channels-images.data-set-info-extractor = ch.systemsx.cisd.openb
genedata-merged-channels-images.data-set-info-extractor.entity-separator = .
genedata-merged-channels-images.data-set-info-extractor.index-of-sample-code = 0
genedata-merged-channels-images.data-set-info-extractor.index-of-data-producer-code =
-genedata-merged-channels-images.data-set-info-extractor.space-code = DEMO
+genedata-merged-channels-images.data-set-info-extractor.space-code = ${import-space-code}
# The extractor class to use for type extraction
genedata-merged-channels-images.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
@@ -330,7 +347,7 @@ genedata-image-analysis-results.data-set-info-extractor = ch.systemsx.cisd.openb
# Separator used to extract the barcode in the data set file name
genedata-image-analysis-results.data-set-info-extractor.entity-separator = .
genedata-image-analysis-results.data-set-info-extractor.index-of-sample-code = 0
-genedata-image-analysis-results.data-set-info-extractor.space-code = DEMO
+genedata-image-analysis-results.data-set-info-extractor.space-code = ${import-space-code}
# The extractor class to use for type extraction
genedata-image-analysis-results.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
--
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