From f6b87d8bcb73f088b1ae093be28fe5b4c4cca36d Mon Sep 17 00:00:00 2001
From: jakubs <jakubs>
Date: Tue, 19 Jun 2012 07:55:43 +0000
Subject: [PATCH] BIS-21 SP-107 add transaction encapsulation to screening v2
dropbox
SVN: 25772
---
...agingDataSetRegistrationTransactionV2.java | 39 +++
...aSetRegistrationTransactionV2Delegate.java | 240 ++++++++++++++++++
.../v2/JythonPlateDataSetHandlerV2.java | 10 +
.../server/dropbox/hcs-simple-test.py | 6 +-
4 files changed, 292 insertions(+), 3 deletions(-)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/IImagingDataSetRegistrationTransactionV2.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/ImagingDataSetRegistrationTransactionV2Delegate.java
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/IImagingDataSetRegistrationTransactionV2.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/IImagingDataSetRegistrationTransactionV2.java
new file mode 100644
index 00000000000..df5939b0cb6
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/IImagingDataSetRegistrationTransactionV2.java
@@ -0,0 +1,39 @@
+/*
+ * Copyright 2012 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.dss.etl.jython.v2;
+
+import java.io.File;
+
+import ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSetRegistrationTransactionV2;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.IImageDataSet;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.SimpleImageDataConfig;
+
+/**
+ *
+ *
+ * @author Jakub Straszewski
+ */
+public interface IImagingDataSetRegistrationTransactionV2 extends
+ IDataSetRegistrationTransactionV2
+{
+ /**
+ * Creates a new image dataset. See {@link SimpleImageDataConfig} documentation for
+ * configuration details.
+ */
+ IImageDataSet createNewImageDataSet(SimpleImageDataConfig imageDataSet,
+ File incomingFolderWithImages);
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/ImagingDataSetRegistrationTransactionV2Delegate.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/ImagingDataSetRegistrationTransactionV2Delegate.java
new file mode 100644
index 00000000000..b3fb113dd72
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/ImagingDataSetRegistrationTransactionV2Delegate.java
@@ -0,0 +1,240 @@
+/*
+ * Copyright 2012 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.dss.etl.jython.v2;
+
+import java.io.File;
+
+import net.lemnik.eodsql.DynamicTransactionQuery;
+
+import ch.systemsx.cisd.etlserver.TopLevelDataSetRegistratorGlobalState;
+import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationPersistentMap;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSet;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSetUpdatable;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.IExperiment;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.IMaterial;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.IProject;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.ISample;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.ISpace;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.IImageDataSet;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.SimpleImageDataConfig;
+import ch.systemsx.cisd.openbis.dss.etl.jython.ImagingDataSetRegistrationTransaction;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IDataSetImmutable;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IExperimentImmutable;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IMaterialImmutable;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IProjectImmutable;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.ISampleImmutable;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.ISearchService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.ISpaceImmutable;
+
+/**
+ * @author Jakub Straszewski
+ */
+public class ImagingDataSetRegistrationTransactionV2Delegate implements
+ IImagingDataSetRegistrationTransactionV2
+{
+ public ImagingDataSetRegistrationTransactionV2Delegate(
+ ImagingDataSetRegistrationTransaction transaction)
+ {
+ this.transaction = transaction;
+ }
+
+ private final ImagingDataSetRegistrationTransaction transaction;
+
+ @Override
+ public IImageDataSet createNewImageDataSet(SimpleImageDataConfig imageDataSet,
+ File incomingFolderWithImages)
+ {
+ return transaction.createNewImageDataSet(imageDataSet, incomingFolderWithImages);
+ }
+
+ @Override
+ public IDataSet createNewDataSet()
+ {
+ return transaction.createNewDataSet();
+ }
+
+ @Override
+ public IDataSet createNewDataSet(String dataSetType)
+ {
+ return transaction.createNewDataSet(dataSetType);
+ }
+
+ @Override
+ public IDataSet createNewDataSet(String dataSetType, String dataSetCode)
+ {
+ return transaction.createNewDataSet(dataSetType, dataSetCode);
+ }
+
+ @Override
+ public IDataSetImmutable getDataSet(String dataSetCode)
+ {
+ return transaction.getDataSet(dataSetCode);
+ }
+
+ @Override
+ public IDataSetUpdatable getDataSetForUpdate(String dataSetCode)
+ {
+ return transaction.getDataSetForUpdate(dataSetCode);
+ }
+
+ @Override
+ public IDataSetUpdatable makeDataSetMutable(IDataSetImmutable dataSet)
+ {
+ return transaction.makeDataSetMutable(dataSet);
+ }
+
+ @Override
+ public ISampleImmutable getSample(String sampleIdentifierString)
+ {
+ return transaction.getSample(sampleIdentifierString);
+ }
+
+ @Override
+ public ISample getSampleForUpdate(String sampleIdentifierString)
+ {
+ return transaction.getSampleForUpdate(sampleIdentifierString);
+ }
+
+ @Override
+ public ISample makeSampleMutable(ISampleImmutable sample)
+ {
+ return transaction.makeSampleMutable(sample);
+ }
+
+ @Override
+ public ISample createNewSample(String sampleIdentifierString, String sampleTypeCode)
+ {
+ return transaction.createNewSample(sampleIdentifierString, sampleTypeCode);
+ }
+
+ @Override
+ public IExperimentImmutable getExperiment(String experimentIdentifierString)
+ {
+ return transaction.getExperiment(experimentIdentifierString);
+ }
+
+ @Override
+ public IExperiment getExperimentForUpdate(String experimentIdentifierString)
+ {
+ return transaction.getExperimentForUpdate(experimentIdentifierString);
+ }
+
+ @Override
+ public IExperiment createNewExperiment(String experimentIdentifierString,
+ String experimentTypeCode)
+ {
+ return transaction.createNewExperiment(experimentIdentifierString, experimentTypeCode);
+ }
+
+ @Override
+ public IProject createNewProject(String projectIdentifier)
+ {
+ return transaction.createNewProject(projectIdentifier);
+ }
+
+ @Override
+ public IProjectImmutable getProject(String projectIdentifier)
+ {
+ return transaction.getProject(projectIdentifier);
+ }
+
+ @Override
+ public ISpace createNewSpace(String spaceCode, String spaceAdminUserIdOrNull)
+ {
+ return transaction.createNewSpace(spaceCode, spaceAdminUserIdOrNull);
+ }
+
+ @Override
+ public ISpaceImmutable getSpace(String spaceCode)
+ {
+ return transaction.getSpace(spaceCode);
+ }
+
+ @Override
+ public IMaterialImmutable getMaterial(String materialCode, String materialType)
+ {
+ return transaction.getMaterial(materialCode, materialType);
+ }
+
+ @Override
+ public IMaterial createNewMaterial(String materialCode, String materialType)
+ {
+ return transaction.createNewMaterial(materialCode, materialType);
+ }
+
+ @Override
+ public String moveFile(String src, IDataSet dst)
+ {
+ return transaction.moveFile(src, dst);
+ }
+
+ @Override
+ public String moveFile(String src, IDataSet dst, String dstInDataset)
+ {
+ return transaction.moveFile(src, dst, dstInDataset);
+ }
+
+ @Override
+ public String createNewDirectory(IDataSet dst, String dirName)
+ {
+ return transaction.createNewDirectory(dst, dirName);
+ }
+
+ @Override
+ public String createNewFile(IDataSet dst, String fileName)
+ {
+ return transaction.createNewFile(dst, fileName);
+ }
+
+ @Override
+ public String createNewFile(IDataSet dst, String dstInDataset, String fileName)
+ {
+ return transaction.createNewFile(dst, dstInDataset, fileName);
+ }
+
+ @Override
+ public ISearchService getSearchService()
+ {
+ return transaction.getSearchService();
+ }
+
+ @Override
+ public DynamicTransactionQuery getDatabaseQuery(String dataSourceName)
+ throws IllegalArgumentException
+ {
+ return transaction.getDatabaseQuery(dataSourceName);
+ }
+
+ @Override
+ public DataSetRegistrationPersistentMap getRegistrationContext()
+ {
+ return transaction.getRegistrationContext();
+ }
+
+ @Override
+ public TopLevelDataSetRegistratorGlobalState getGlobalState()
+ {
+ return transaction.getGlobalState();
+ }
+
+ @Override
+ public File getIncoming()
+ {
+ return transaction.getIncoming();
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/JythonPlateDataSetHandlerV2.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/JythonPlateDataSetHandlerV2.java
index 21336ee67c0..3445ee6d0f9 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/JythonPlateDataSetHandlerV2.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/JythonPlateDataSetHandlerV2.java
@@ -27,7 +27,9 @@ import ch.systemsx.cisd.etlserver.TopLevelDataSetRegistratorGlobalState;
import ch.systemsx.cisd.etlserver.registrator.DataSetFile;
import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationService;
import ch.systemsx.cisd.etlserver.registrator.IDataSetRegistrationDetailsFactory;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSetRegistrationTransaction;
import ch.systemsx.cisd.etlserver.registrator.api.v1.impl.DataSetRegistrationTransaction;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSetRegistrationTransactionV2;
import ch.systemsx.cisd.etlserver.registrator.api.v2.JythonDataSetRegistrationServiceV2;
import ch.systemsx.cisd.etlserver.registrator.api.v2.JythonTopLevelDataSetHandlerV2;
import ch.systemsx.cisd.etlserver.registrator.recovery.AutoRecoverySettings;
@@ -92,4 +94,12 @@ public class JythonPlateDataSetHandlerV2 extends JythonTopLevelDataSetHandlerV2<
}
};
}
+
+ @Override
+ protected IDataSetRegistrationTransactionV2 wrapTransaction(
+ IDataSetRegistrationTransaction transaction)
+ {
+ return new ImagingDataSetRegistrationTransactionV2Delegate(
+ (ImagingDataSetRegistrationTransaction) transaction);
+ }
}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/dropbox/hcs-simple-test.py b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/dropbox/hcs-simple-test.py
index e420301432a..4e760cacd0e 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/dropbox/hcs-simple-test.py
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/dropbox/hcs-simple-test.py
@@ -57,15 +57,15 @@ class MyImageDataSetConfig(SimpleImageDataConfig):
def getTileGeometry(self, imageTokens, maxTileNumber):
return Geometry.createFromRowColDimensions(maxTileNumber / 3, 3)
-def process():
+def process(transaction):
+ incoming = transaction.getIncoming()
if incoming.isDirectory():
imageDataset = MyImageDataSetConfig()
imageDataset.setRawImageDatasetType()
imageDataset.setGenerateThumbnails(True)
imageDataset.setUseImageMagicToGenerateThumbnails(False)
imageDataset.setPlate(SPACE_CODE, PLATE_CODE)
- registrationDetails = factory.createImageRegistrationDetails(imageDataset, incoming)
plate = create_plate_if_needed(transaction)
- dataset = transaction.createNewDataSet(registrationDetails);
+ dataset = transaction.createNewImageDataSet(imageDataset, incoming);
dataset.setSample(plate)
transaction.moveFile(incoming.getPath(), dataset);
--
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