From 35ecd8fcbb2145d063ba17ca0c9533e3c3808887 Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Tue, 5 Apr 2011 14:31:58 +0000
Subject: [PATCH] LMS-2164 bugfixes in iBrain dropboxes
SVN: 20658
---
.../dropboxes/scripts/commonDropbox.py | 8 ++++++--
.../scripts/hcs_analysis_cell_features_csv.py | 6 +++++-
.../scripts/hcs_analysis_cell_features_mat.py | 6 +++++-
.../scripts/hcs_analysis_well_features.py | 6 +++++-
.../scripts/hcs_analysis_well_quality.py | 6 +++++-
.../dropboxes/scripts/hcs_image_overview.py | 8 ++++++--
.../dropboxes/scripts/hcs_image_raw.py | 19 +++++++++++--------
.../scripts/hcs_image_segmentation.py | 12 ++++++++----
8 files changed, 51 insertions(+), 20 deletions(-)
diff --git a/integration-tests/templates/data-ibrain2/dropboxes/scripts/commonDropbox.py b/integration-tests/templates/data-ibrain2/dropboxes/scripts/commonDropbox.py
index 0dd550dfabe..abd66bdc8ab 100755
--- a/integration-tests/templates/data-ibrain2/dropboxes/scripts/commonDropbox.py
+++ b/integration-tests/templates/data-ibrain2/dropboxes/scripts/commonDropbox.py
@@ -77,7 +77,7 @@ class AbstractMetadataParser(AbstractPropertiesParser):
class AcquiredDatasetMetadataParser(AbstractMetadataParser):
PLATE_CODE_PRPOPERTY = "barcode"
INSTRUMENT_PROPERTY = "instrument.id"
- TIMESTAMP_PROPERTY = "timestamp" # not used
+ TIMESTAMP_PROPERTY = "timestamp"
# All dataset properties.
# Returns:
@@ -86,6 +86,7 @@ class AcquiredDatasetMetadataParser(AbstractMetadataParser):
properties = AbstractPropertiesParser.getDatasetPropertiesIter(self)
properties = [ (key, value) for (key, value) in properties if key != "ibrain2.assay.id" ]
properties.append((self.INSTRUMENT_PROPERTY, self.get(self.INSTRUMENT_PROPERTY)))
+ properties.append((self.TIMESTAMP_PROPERTY, self.get(self.TIMESTAMP_PROPERTY)))
return properties
def getPlateCode(self):
@@ -254,7 +255,10 @@ def createSuccessStatus(iBrain2DatasetId, dataset, incomingPath):
RegistrationConfirmationUtils().createSuccessStatus(iBrain2DatasetId, datasetCode, incomingPath)
def createFailureStatus(iBrain2DatasetId, throwable, incoming):
- RegistrationConfirmationUtils().createFailureStatus(iBrain2DatasetId, throwable.getMessage(), incoming.getPath())
+ msg = throwable.getMessage()
+ if msg == None:
+ msg = throwable.toString()
+ RegistrationConfirmationUtils().createFailureStatus(iBrain2DatasetId, msg, incoming.getPath())
# -------------- TODO: remove tests
diff --git a/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_analysis_cell_features_csv.py b/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_analysis_cell_features_csv.py
index a3276bb96e4..f66dfcbd1e4 100755
--- a/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_analysis_cell_features_csv.py
+++ b/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_analysis_cell_features_csv.py
@@ -10,8 +10,12 @@ reload(commonDropbox)
# so that the rollback can use it as well.
iBrain2DatasetId = None
-def rollback_transaction(service, transaction, algorithmRunner, throwable):
+def rollback_service(service, throwable):
+ global iBrain2DatasetId
commonDropbox.createFailureStatus(iBrain2DatasetId, throwable, incoming)
+
+def rollback_transaction(service, transaction, algorithmRunner, throwable):
+ rollback_service(service, throwable)
if incoming.isDirectory():
metadataParser = commonDropbox.DerivedDatasetMetadataParser(incoming.getPath())
diff --git a/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_analysis_cell_features_mat.py b/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_analysis_cell_features_mat.py
index aafd2dce175..a7dfb919cde 100755
--- a/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_analysis_cell_features_mat.py
+++ b/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_analysis_cell_features_mat.py
@@ -10,8 +10,12 @@ reload(commonDropbox)
# so that the rollback can use it as well.
iBrain2DatasetId = None
-def rollback_transaction(service, transaction, algorithmRunner, throwable):
+def rollback_service(service, throwable):
+ global iBrain2DatasetId
commonDropbox.createFailureStatus(iBrain2DatasetId, throwable, incoming)
+
+def rollback_transaction(service, transaction, algorithmRunner, throwable):
+ rollback_service(service, throwable)
if incoming.isDirectory():
metadataParser = commonDropbox.DerivedDatasetMetadataParser(incoming.getPath())
diff --git a/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_analysis_well_features.py b/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_analysis_well_features.py
index 1558b858e53..4c6ba29fba3 100755
--- a/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_analysis_well_features.py
+++ b/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_analysis_well_features.py
@@ -50,8 +50,12 @@ def register(incomingPath):
dataset.setFileFormatType('CSV')
commonDropbox.registerDerivedDataset(state, transaction, dataset, incoming, metadataParser)
-def rollback_transaction(service, transaction, algorithmRunner, throwable):
+def rollback_service(service, throwable):
+ global iBrain2DatasetId
commonDropbox.createFailureStatus(iBrain2DatasetId, throwable, incoming)
+
+def rollback_transaction(service, transaction, algorithmRunner, throwable):
+ rollback_service(service, throwable)
if incoming.isDirectory():
register(incoming.getPath())
\ No newline at end of file
diff --git a/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_analysis_well_quality.py b/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_analysis_well_quality.py
index bb97d6e3f4a..df79b0349a2 100755
--- a/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_analysis_well_quality.py
+++ b/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_analysis_well_quality.py
@@ -37,8 +37,12 @@ def register(incomingPath):
dataset.setFileFormatType('CSV')
commonDropbox.registerDerivedDataset(state, transaction, dataset, incoming, metadataParser)
-def rollback_transaction(service, transaction, algorithmRunner, throwable):
+def rollback_service(service, throwable):
+ global iBrain2DatasetId
commonDropbox.createFailureStatus(iBrain2DatasetId, throwable, incoming)
+
+def rollback_transaction(service, transaction, algorithmRunner, throwable):
+ rollback_service(service, throwable)
if incoming.isDirectory():
register(incoming.getPath())
\ No newline at end of file
diff --git a/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_image_overview.py b/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_image_overview.py
index a596c43cc6d..873126de5e3 100755
--- a/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_image_overview.py
+++ b/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_image_overview.py
@@ -31,9 +31,13 @@ def register(incomingPath):
commonDropbox.setImageDatasetPropertiesAndRegister(imageDataset, metadataParser, incoming, service, factory)
-def rollback_transaction(service, transaction, algorithmRunner, throwable):
+def rollback_service(service, throwable):
+ global iBrain2DatasetId
commonDropbox.createFailureStatus(iBrain2DatasetId, throwable, incoming)
-
+
+def rollback_transaction(service, transaction, algorithmRunner, throwable):
+ rollback_service(service, throwable)
+
if incoming.isDirectory():
register(incoming.getPath())
diff --git a/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_image_raw.py b/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_image_raw.py
index 7f639112fd6..3a6e287e10e 100755
--- a/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_image_raw.py
+++ b/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_image_raw.py
@@ -11,6 +11,8 @@ PLATE_TYPE_CODE = "PLATE"
SIRNA_EXP_TYPE = "SIRNA_HCS"
PLATE_GEOMETRY_PROPERTY_CODE = "$PLATE_GEOMETRY"
+iBrain2DatasetId = None
+
def createPlateWithExperimentIfNeeded(transaction, assayParser, plateCode, spaceCode, plateGeometry):
projectCode = assayParser.get(assayParser.EXPERIMENTER_PROPERTY)
experiment = assayParser.get(assayParser.ASSAY_ID_PROPERTY)
@@ -38,9 +40,13 @@ def createPlateWithExperimentIfNeeded(transaction, assayParser, plateCode, space
plate.setExperiment(experiment)
return plate
-
-iBrain2DatasetId = None
-
+def rollback_service(service, throwable):
+ global iBrain2DatasetId
+ commonDropbox.createFailureStatus(iBrain2DatasetId, throwable, incoming)
+
+def rollback_transaction(service, transaction, algorithmRunner, throwable):
+ rollback_service(service, throwable)
+
if incoming.isDirectory():
incomingPath = incoming.getPath()
metadataParser = commonDropbox.AcquiredDatasetMetadataParser(incomingPath)
@@ -69,8 +75,5 @@ if incoming.isDirectory():
dataset = tr.createNewDataSet(imageRegistrationDetails)
dataset.setSample(plate)
imageDataSetFolder = tr.moveFile(incomingPath, dataset)
- tr.commit()
- commonDropbox.createSuccessStatus(iBrain2DatasetId, dataset, incomingPath)
-
-def rollback_transaction(service, transaction, algorithmRunner, throwable):
- commonDropbox.createFailureStatus(iBrain2DatasetId, throwable, incoming)
\ No newline at end of file
+ if tr.commit():
+ commonDropbox.createSuccessStatus(iBrain2DatasetId, dataset, incomingPath)
\ No newline at end of file
diff --git a/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_image_segmentation.py b/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_image_segmentation.py
index a0d9f775c2d..a05c08dde09 100755
--- a/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_image_segmentation.py
+++ b/integration-tests/templates/data-ibrain2/dropboxes/scripts/hcs_image_segmentation.py
@@ -12,6 +12,13 @@ reload(commonDropbox)
# so that the rollback can use it as well.
iBrain2DatasetId = None
+def rollback_service(service, throwable):
+ global iBrain2DatasetId
+ commonDropbox.createFailureStatus(iBrain2DatasetId, throwable, incoming)
+
+def rollback_transaction(service, transaction, algorithmRunner, throwable):
+ rollback_service(service, throwable)
+
def register(incomingPath):
metadataParser = commonDropbox.DerivedDatasetMetadataParser(incomingPath)
global iBrain2DatasetId
@@ -34,9 +41,6 @@ def register(incomingPath):
imageDataset.setOriginalDataStorageFormat(OriginalDataStorageFormat.HDF5)
commonDropbox.setImageDatasetPropertiesAndRegister(imageDataset, metadataParser, incoming, service, factory)
-
-def rollback_transaction(service, transaction, algorithmRunner, throwable):
- commonDropbox.createFailureStatus(iBrain2DatasetId, throwable, incoming)
-
+
if incoming.isDirectory():
register(incoming.getPath())
--
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