From 6c889975afd0e6546c7e033dbd1ddb062013ae37 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Tue, 28 Feb 2012 12:40:07 +0000
Subject: [PATCH] LMS-2612 add disabled-core-plugins property, remove jython
drop box because it hase been moved to core-plugins
SVN: 24583
---
.../dist/etc/service.properties | 2 +
.../installer/data/dropboxes/hcs-dropbox.py | 84 -------------------
2 files changed, 2 insertions(+), 84 deletions(-)
delete mode 100644 openbis_standard_technologies/dist/tarball/installer/data/dropboxes/hcs-dropbox.py
diff --git a/openbis_standard_technologies/dist/etc/service.properties b/openbis_standard_technologies/dist/etc/service.properties
index 50dc38d3135..74885b91639 100644
--- a/openbis_standard_technologies/dist/etc/service.properties
+++ b/openbis_standard_technologies/dist/etc/service.properties
@@ -67,6 +67,8 @@ mail.smtp.host = file://${root-dir}
# mail.smtp.user =
# mail.smtp.password =
+disabled-core-plugins = $DISABLED_TECHNOLOGIES
+
# ---------------------------------------------------------------------------
# (optional) archiver configuration
# ---------------------------------------------------------------------------
diff --git a/openbis_standard_technologies/dist/tarball/installer/data/dropboxes/hcs-dropbox.py b/openbis_standard_technologies/dist/tarball/installer/data/dropboxes/hcs-dropbox.py
deleted file mode 100644
index 3d6b051d1ae..00000000000
--- a/openbis_standard_technologies/dist/tarball/installer/data/dropboxes/hcs-dropbox.py
+++ /dev/null
@@ -1,84 +0,0 @@
-import os
-from ch.systemsx.cisd.openbis.dss.etl.dto.api.v1 import SimpleImageDataConfig
-from ch.systemsx.cisd.openbis.dss.etl.dto.api.v1 import ImageMetadata
-from ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto import Geometry
-
-SPACE_CODE = "TEST"
-PROJECT_CODE = "TEST-PROJECT"
-PROJECT_ID = "/%(SPACE_CODE)s/%(PROJECT_CODE)s" % vars()
-EXPERIMENT_CODE = "DEMO-EXP-HCS"
-EXPERIMENT_ID = "/%(SPACE_CODE)s/%(PROJECT_CODE)s/%(EXPERIMENT_CODE)s" % vars()
-
-PLATE_CODE = "PLATE1"
-PLATE_ID = "/%(SPACE_CODE)s/%(PLATE_CODE)s" % vars()
-PLATE_GEOMETRY_PROPERTY_CODE = "$PLATE_GEOMETRY"
-PLATE_GEOMETRY = "384_WELLS_16X24"
-
-
-def create_space_if_needed(transaction):
- space = transaction.getSpace(SPACE_CODE)
- if None == space:
- space = transaction.createNewSpace(SPACE_CODE, None)
- space.setDescription("A demo space")
-
-def create_project_if_needed(transaction):
- project = transaction.getProject(PROJECT_ID)
- if None == project:
- create_space_if_needed(transaction)
- project = transaction.createNewProject(PROJECT_ID)
- project.setDescription("A demo project")
-
-def create_experiment_if_needed(transaction):
- """ Get the specified experiment or register it if necessary """
- exp = transaction.getExperiment(EXPERIMENT_ID)
- if None == exp:
- create_project_if_needed(transaction)
- print 'Creating new experiment : ' + EXPERIMENT_ID
- exp = transaction.createNewExperiment(EXPERIMENT_ID, 'SIRNA_HCS')
- exp.setPropertyValue("DESCRIPTION", "A sample experiment")
-
- return exp
-
-def create_plate_if_needed(transaction):
- """ Get the specified sample or register it if necessary """
-
- samp = transaction.getSample(PLATE_ID)
-
- if None == samp:
- exp = create_experiment_if_needed(transaction)
- samp = transaction.createNewSample(PLATE_ID, 'PLATE')
- samp.setPropertyValue(PLATE_GEOMETRY_PROPERTY_CODE, PLATE_GEOMETRY)
- samp.setExperiment(exp)
-
- return samp
-
-
-class MyImageDataSetConfig(SimpleImageDataConfig):
- def extractImageMetadata(self, imagePath):
-
- basename = os.path.splitext(imagePath)[0]
- (plate, well, tile, channelCode) = basename.split("_")
-
- image_tokens = ImageMetadata()
- image_tokens.well = well
- try:
- image_tokens.tileNumber = int(tile)
- except ValueError:
- raise Exception("Cannot parse field number from '" + tile + "' in '" + basename + "' file name.")
-
- image_tokens.channelCode = channelCode
- return image_tokens
-
- def getTileGeometry(self, imageTokens, maxTileNumber):
- return Geometry.createFromRowColDimensions(maxTileNumber / 3, 3)
-
-if incoming.isDirectory():
- imageDataset = MyImageDataSetConfig()
- imageDataset.setRawImageDatasetType()
- imageDataset.setPlate(SPACE_CODE, PLATE_CODE)
- registrationDetails = factory.createImageRegistrationDetails(imageDataset, incoming)
- transaction = service.transaction(incoming, factory)
- plate = create_plate_if_needed(transaction)
- dataset = transaction.createNewDataSet(registrationDetails);
- dataset.setSample(plate)
- transaction.moveFile(incoming.getPath(), dataset);
--
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