From fbf74cf5513b04b70e8d1eafc156c1f81cce38c8 Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Wed, 16 Mar 2011 09:30:59 +0000
Subject: [PATCH] LMS-2069 iBrain2 dropboxes: image quality dropbox
SVN: 20355
---
.../dss-dropboxes-service.properties | 7 +----
.../scripts/hcs_analysis_well_quality.py | 28 +++++++++++++++----
2 files changed, 23 insertions(+), 12 deletions(-)
diff --git a/integration-tests/templates/data-ibrain2/dss-dropboxes-service.properties b/integration-tests/templates/data-ibrain2/dss-dropboxes-service.properties
index f8eeeef7b61..8675a121310 100644
--- a/integration-tests/templates/data-ibrain2/dss-dropboxes-service.properties
+++ b/integration-tests/templates/data-ibrain2/dss-dropboxes-service.properties
@@ -5,6 +5,7 @@ ibrain2-dropboxes-dir = ${root}/incoming
staging-dir = ${root}/tmp
scripts-dir = ${root}/scripts
+
# --- hcs_image_raw ------------
hcs_image_raw.incoming-dir = ${ibrain2-dropboxes-dir}/hcs_image_raw
@@ -70,11 +71,6 @@ hcs_analysis_well_quality.staging-dir = ${staging-dir}
hcs_analysis_well_quality.storage-processor = ch.systemsx.cisd.openbis.dss.etl.featurevector.FeatureVectorStorageProcessor
hcs_analysis_well_quality.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
hcs_analysis_well_quality.storage-processor.data-source = imaging-db
-hcs_analysis_well_quality.storage-processor.separator = ,
-hcs_analysis_well_quality.storage-processor.ignore-comments = true
-hcs_analysis_well_quality.storage-processor.well-name-col-is-alphanum = true
-hcs_analysis_well_quality.storage-processor.well-name-row = File_Name
-hcs_analysis_well_quality.storage-processor.well-name-col = File_Name
# --- hcs_analysis_well_features -----------
@@ -101,4 +97,3 @@ hcs_analysis_well_metadata.staging-dir = ${staging-dir}
hcs_analysis_well_metadata.storage-processor = ch.systemsx.cisd.openbis.dss.etl.featurevector.FeatureVectorStorageProcessor
hcs_analysis_well_metadata.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
hcs_analysis_well_metadata.storage-processor.data-source = imaging-db
-
diff --git a/integration-tests/templates/data-ibrain2/scripts/hcs_analysis_well_quality.py b/integration-tests/templates/data-ibrain2/scripts/hcs_analysis_well_quality.py
index ed49cae01e7..bb97d6e3f4a 100755
--- a/integration-tests/templates/data-ibrain2/scripts/hcs_analysis_well_quality.py
+++ b/integration-tests/templates/data-ibrain2/scripts/hcs_analysis_well_quality.py
@@ -2,6 +2,7 @@
import commonImageDropbox
import commonDropbox
+from java.util import Properties
reload(commonImageDropbox)
reload(commonDropbox)
@@ -10,17 +11,32 @@ reload(commonDropbox)
# so that the rollback can use it as well.
iBrain2DatasetId = None
+def rollback_transaction(service, transaction, algorithmRunner, throwable):
+ commonDropbox.createFailureStatus(iBrain2DatasetId, throwable, incoming)
+
+def getConfigurationProperties():
+ config = Properties()
+ config.setProperty("separator", ",")
+ config.setProperty("well-name-row", "File_Name")
+ config.setProperty("well-name-col", "File_Name")
+ config.setProperty("well-name-col-is-alphanum", "true")
+ return config
+
def register(incomingPath):
metadataParser = commonDropbox.DerivedDatasetMetadataParser(incomingPath)
+ global iBrain2DatasetId
iBrain2DatasetId = metadataParser.getIBrain2DatasetId()
- openbisDatasetParent = metadataParser.getParentDatasetPermId()
- (space, plate) = commonDropbox.tryGetConnectedPlate(state, openbisDatasetParent, iBrain2DatasetId, incomingPath)
- if plate == None:
- return
-
- #TODO: finish me !!!!
+ transaction = service.transaction(incoming, factory)
+ configProps = getConfigurationProperties()
+ incomingCsvFile = commonDropbox.findCSVFile(incomingPath)
+ analysisRegistrationDetails = factory.createFeatureVectorRegistrationDetails(incomingCsvFile, configProps)
+ dataset = transaction.createNewDataSet(analysisRegistrationDetails)
+ dataset.setDataSetType('HCS_ANALYSIS_WELL_QUALITY')
+ dataset.setFileFormatType('CSV')
+ commonDropbox.registerDerivedDataset(state, transaction, dataset, incoming, metadataParser)
+
def rollback_transaction(service, transaction, algorithmRunner, throwable):
commonDropbox.createFailureStatus(iBrain2DatasetId, throwable, incoming)
--
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